Merge conflicts
This commit is contained in:
jtclemm
@ -101,6 +101,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(extract_setting);
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ADDSYM(extract_global_datatype);
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ADDSYM(extract_global);
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ADDSYM(extract_pair_dimension);
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ADDSYM(extract_pair);
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ADDSYM(map_atom);
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ADDSYM(extract_atom_datatype);
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@ -148,6 +150,7 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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ADDSYM(config_has_png_support);
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ADDSYM(config_has_jpeg_support);
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ADDSYM(config_has_ffmpeg_support);
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ADDSYM(config_has_curl_support);
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ADDSYM(config_has_exceptions);
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ADDSYM(config_has_package);
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@ -144,11 +144,13 @@ struct _liblammpsplugin {
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int (*get_mpi_comm)(void *);
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int (*extract_setting)(void *, const char *);
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int *(*extract_global_datatype)(void *, const char *);
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int (*extract_global_datatype)(void *, const char *);
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void *(*extract_global)(void *, const char *);
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void *(*map_atom)(void *, const void *);
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int (*extract_pair_dimension)(void *, const char *);
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void *(*extract_pair)(void *, const char *);
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int (*map_atom)(void *, const void *);
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int *(*extract_atom_datatype)(void *, const char *);
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int (*extract_atom_datatype)(void *, const char *);
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void *(*extract_atom)(void *, const char *);
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void *(*extract_compute)(void *, const char *, int, int);
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@ -201,6 +203,7 @@ struct _liblammpsplugin {
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int (*config_has_png_support)();
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int (*config_has_jpeg_support)();
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int (*config_has_ffmpeg_support)();
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int (*config_has_curl_support)();
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int (*config_has_exceptions)();
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int (*config_has_package)(const char *);
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@ -5,9 +5,9 @@ dimension 3
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atom_style full
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processors * * 1
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pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
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pair_style lj/spica/coul/long 15.0
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bond_style harmonic
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angle_style sdk # compatible with "spica"
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angle_style spica
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special_bonds lj/coul 0.0 0.0 1.0
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read_data data.sds.gz
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@ -1,629 +0,0 @@
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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14 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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reading bonds ...
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1365 bonds
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reading angles ...
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786 angles
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reading dihedrals ...
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207 dihedrals
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reading impropers ...
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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group peptide type <= 12
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84 atoms in group peptide
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group one id 2 4 5 6
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4 atoms in group one
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group two id 80 82 83 84
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4 atoms in group two
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group ref id 37
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1 atoms in group ref
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group colvar union one two ref
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9 atoms in group colvar
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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shell "rm -f out*.colvars.*"
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fix 2 all colvars peptide.colvars
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fix 2a ref setforce 0.0 0.0 0.0
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_2
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thermo 10
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.268725
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0228209
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estimated relative force accuracy = 6.87243e-05
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using double precision FFTs
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3d grid and FFT values/proc = 10648 3375
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Neighbor list info ...
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update every 1 steps, delay 5 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmm/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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colvars: Creating proxy instance
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colvars: ----------------------------------------------------------------------
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colvars: Initializing the collective variables module, version 2018-11-16.
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colvars: Please cite Fiorin et al, Mol Phys 2013:
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colvars: https://doi.org/10.1080/00268976.2013.813594
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colvars: in any publication based on this calculation.
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colvars: SMP parallelism is available.
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colvars: Using LAMMPS interface, version 2018-08-29.
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colvars: ----------------------------------------------------------------------
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colvars: Reading new configuration from file "peptide.colvars":
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colvars: # smp = on [default]
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colvars: # colvarsTrajFrequency = 1
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colvars: # colvarsRestartFrequency = 1000
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colvars: # scriptedColvarForces = off [default]
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colvars: # scriptingAfterBiases = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = "one"
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colvars: Initializing a new "distance" component.
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colvars: # name = "" [default]
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # scalable = on [default]
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colvars: Initializing atom group "group1".
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colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
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colvars: Initializing atom group "group2".
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colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
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colvars: # oneSiteSystemForce = off [default]
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colvars: # oneSiteTotalForce = off [default]
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colvars: All components initialized.
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colvars: # timeStepFactor = 1 [default]
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputTotalForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: # subtractAppliedForce = off [default]
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colvars: # runAve = off [default]
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colvars: # corrFunc = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = "two"
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colvars: Initializing a new "distance" component.
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colvars: # name = "" [default]
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # scalable = on [default]
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colvars: Initializing atom group "group1".
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colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
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colvars: Initializing atom group "group2".
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colvars: # name = "" [default]
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colvars: # centerReference = off [default]
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colvars: # rotateReference = off [default]
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colvars: # atomsOfGroup = "" [default]
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colvars: # indexGroup = "" [default]
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colvars: # psfSegID = [default]
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colvars: # atomsFile = "" [default]
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colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
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colvars: # enableForces = on [default]
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colvars: # enableFitGradients = on [default]
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colvars: # printAtomIDs = off [default]
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colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
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colvars: # oneSiteSystemForce = off [default]
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colvars: # oneSiteTotalForce = off [default]
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colvars: All components initialized.
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colvars: # timeStepFactor = 1 [default]
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputTotalForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: # subtractAppliedForce = off [default]
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colvars: # runAve = off [default]
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colvars: # corrFunc = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables initialized, 2 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new "harmonic" instance.
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colvars: # name = "h_pot"
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colvars: # colvars = { one, two }
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colvars: # outputEnergy = off [default]
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colvars: # timeStepFactor = 1 [default]
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colvars: # writeTISamples = off [default]
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colvars: # writeTIPMF = off [default]
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colvars: # centers = { 10, 10 }
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colvars: # targetCenters = { 10, 10 } [default]
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colvars: # outputCenters = off [default]
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colvars: # forceConstant = 100
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colvars: # targetForceConstant = -1 [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables biases initialized, 1 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables module (re)initialized.
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colvars: ----------------------------------------------------------------------
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colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
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colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
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colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
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colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
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colvars: The restart output state file will be "rest.colvars.state".
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colvars: The final output state file will be "out.colvars.state".
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colvars: Writing to colvar trajectory file "out.colvars.traj".
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colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
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colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
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colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
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colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
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colvars: Performing analysis.
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond f_2
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0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
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10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
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20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
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||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
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40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
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||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
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||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
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70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
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||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
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90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
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||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
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||||
6 0.996996 1.00568e-05
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||||
8 1.08 6.02345e-06
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||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
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||||
14 0.959996 0
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||||
18 0.957198 3.36079e-05
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||||
31 104.52 0.0030599
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||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
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colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.17304 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.952 ns/day, 3.018 hours/ns, 46.018 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5817 | 1.5817 | 1.5817 | 0.0 | 72.79
|
||||
Bond | 0.0031469 | 0.0031469 | 0.0031469 | 0.0 | 0.14
|
||||
Kspace | 0.17366 | 0.17366 | 0.17366 | 0.0 | 7.99
|
||||
Neigh | 0.37354 | 0.37354 | 0.37354 | 0.0 | 17.19
|
||||
Comm | 0.013652 | 0.013652 | 0.013652 | 0.0 | 0.63
|
||||
Output | 0.00026059 | 0.00026059 | 0.00026059 | 0.0 | 0.01
|
||||
Modify | 0.025484 | 0.025484 | 0.025484 | 0.0 | 1.17
|
||||
Other | | 0.001615 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||
140 253.85111 -5452.1838 -6473.4522 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4727 -6541.7817 1051.3091 -6646.6076 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4424 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3253 -6550.1124 999.78705 -6661.4235 26.200127 3.4336038
|
||||
190 250.80862 -5555.2554 -6564.2836 1009.0282 -6666.164 25.53634 3.3494288
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 2.03298 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 8.500 ns/day, 2.824 hours/ns, 49.189 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5975 | 1.5975 | 1.5975 | 0.0 | 78.58
|
||||
Bond | 0.0033164 | 0.0033164 | 0.0033164 | 0.0 | 0.16
|
||||
Kspace | 0.17349 | 0.17349 | 0.17349 | 0.0 | 8.53
|
||||
Neigh | 0.21971 | 0.21971 | 0.21971 | 0.0 | 10.81
|
||||
Comm | 0.012045 | 0.012045 | 0.012045 | 0.0 | 0.59
|
||||
Output | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.01
|
||||
Modify | 0.025034 | 0.025034 | 0.025034 | 0.0 | 1.23
|
||||
Other | | 0.001596 | | | 0.08
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708083 ave 708083 max 708083 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.335
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: Setting initial step number from LAMMPS: 200
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8287 -6674.0845 24.804906 7.1387574
|
||||
210 253.15303 -5538.5615 -6557.0215 1018.46 -6672.0498 37.67662 0.61219496
|
||||
220 245.19621 -5522.519 -6508.9679 986.44888 -6628.1899 36.657688 0.04864338
|
||||
230 258.69884 -5495.7275 -6536.4988 1040.7713 -6658.2885 34.857911 0.22092547
|
||||
240 260.79635 -5469.8678 -6519.0776 1049.2098 -6624.1801 31.576951 3.7574816
|
||||
250 269.07527 -5438.3946 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600014
|
||||
260 266.01049 -5397.3485 -6467.5353 1070.1868 -6580.2897 26.871917 8.3323097
|
||||
270 272.81313 -5350.882 -6448.4365 1097.5545 -6563.8231 23.114195 10.973131
|
||||
280 279.42263 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644027 8.5490492
|
||||
290 286.85172 -5260.841 -6414.8741 1154.0331 -6515.6798 28.574838 5.9100133
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79792e-05
|
||||
6 0.997005 1.02512e-05
|
||||
8 1.08 1.85102e-05
|
||||
10 1.111 9.98839e-06
|
||||
12 1.08 8.84111e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.8445e-05
|
||||
31 104.52 0.00168383
|
||||
300 291.52798 -5216.288 -6389.1341 1172.8462 -6503.1276 27.889154 2.2482459
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 2.07171 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 8.341 ns/day, 2.877 hours/ns, 48.269 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6047 | 1.6047 | 1.6047 | 0.0 | 77.46
|
||||
Bond | 0.0031033 | 0.0031033 | 0.0031033 | 0.0 | 0.15
|
||||
Kspace | 0.17325 | 0.17325 | 0.17325 | 0.0 | 8.36
|
||||
Neigh | 0.25117 | 0.25117 | 0.25117 | 0.0 | 12.12
|
||||
Comm | 0.012173 | 0.012173 | 0.012173 | 0.0 | 0.59
|
||||
Output | 0.00026488 | 0.00026488 | 0.00026488 | 0.0 | 0.01
|
||||
Modify | 0.025317 | 0.025317 | 0.025317 | 0.0 | 1.22
|
||||
Other | | 0.001731 | | | 0.08
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11296 ave 11296 max 11296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708152 ave 708152 max 708152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.369
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:06
|
||||
@ -1,629 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.614168 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 28.136 ns/day, 0.853 hours/ns, 162.822 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40413 | 0.41468 | 0.42573 | 1.4 | 67.52
|
||||
Bond | 0.00056815 | 0.0011595 | 0.0017791 | 1.6 | 0.19
|
||||
Kspace | 0.056367 | 0.066512 | 0.076213 | 3.3 | 10.83
|
||||
Neigh | 0.095025 | 0.09507 | 0.095124 | 0.0 | 15.48
|
||||
Comm | 0.015385 | 0.015831 | 0.01623 | 0.2 | 2.58
|
||||
Output | 0.00026512 | 0.00034493 | 0.00057554 | 0.0 | 0.06
|
||||
Modify | 0.01938 | 0.019431 | 0.019474 | 0.0 | 3.16
|
||||
Other | | 0.001141 | | | 0.19
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031592
|
||||
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0941 -6559.6493 1019.5552 -6656.6677 23.293812 10.290217
|
||||
180 248.51161 -5550.3253 -6550.1124 999.78704 -6661.4235 26.200127 3.4336037
|
||||
190 250.80862 -5555.2553 -6564.2834 1009.0282 -6666.1638 25.53634 3.3494287
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
||||
colvars: Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.569733 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 30.330 ns/day, 0.791 hours/ns, 175.521 timesteps/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40512 | 0.41306 | 0.42363 | 1.3 | 72.50
|
||||
Bond | 0.00061107 | 0.001151 | 0.0017512 | 1.4 | 0.20
|
||||
Kspace | 0.054393 | 0.063988 | 0.07198 | 3.0 | 11.23
|
||||
Neigh | 0.056063 | 0.056079 | 0.05609 | 0.0 | 9.84
|
||||
Comm | 0.013584 | 0.014145 | 0.014649 | 0.3 | 2.48
|
||||
Output | 0.00026965 | 0.00042897 | 0.00090265 | 0.0 | 0.08
|
||||
Modify | 0.019253 | 0.019257 | 0.01926 | 0.0 | 3.38
|
||||
Other | | 0.001623 | | | 0.28
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177021 ave 182259 max 172089 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.335
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "two"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 1, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 2 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one, two }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10, 10 }
|
||||
colvars: # targetCenters = { 10, 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 1.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 1.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Restarting from file "out.colvars.state".
|
||||
colvars: Restarting collective variable "one" from value: 10.0128
|
||||
colvars: Restarting collective variable "two" from value: 9.62236
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "out2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "out2.colvars.traj".
|
||||
colvars: Setting initial step number from LAMMPS: 200
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 1.81266e-06
|
||||
6 0.997 7.79424e-07
|
||||
8 1.08 1.08903e-06
|
||||
10 1.111 2.96503e-07
|
||||
12 1.08 4.69038e-07
|
||||
14 0.960001 0
|
||||
18 0.957201 3.76471e-06
|
||||
31 104.52 0.000411055
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.86 | 16.06 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2539 1011.8288 -6674.0845 24.804905 7.1387572
|
||||
210 253.15304 -5538.5615 -6557.0215 1018.46 -6672.0498 37.676621 0.61219486
|
||||
220 245.19621 -5522.5189 -6508.9678 986.44888 -6628.1898 36.657688 0.048643368
|
||||
230 258.69885 -5495.7276 -6536.4989 1040.7713 -6658.2887 34.857911 0.22092541
|
||||
240 260.79635 -5469.8677 -6519.0775 1049.2098 -6624.18 31.576952 3.7574818
|
||||
250 269.07527 -5438.3947 -6520.9115 1082.5167 -6616.4384 25.447674 8.6600013
|
||||
260 266.0105 -5397.3486 -6467.5354 1070.1868 -6580.2898 26.871917 8.3323096
|
||||
270 272.81314 -5350.8819 -6448.4364 1097.5545 -6563.823 23.114195 10.973131
|
||||
280 279.42263 -5307.9799 -6432.125 1124.1452 -6557.3367 33.644027 8.5490488
|
||||
290 286.8517 -5260.8409 -6414.874 1154.0331 -6515.6797 28.574839 5.9100135
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 1.79792e-05
|
||||
6 0.997005 1.02512e-05
|
||||
8 1.08 1.85102e-05
|
||||
10 1.111 9.98838e-06
|
||||
12 1.08 8.84113e-06
|
||||
14 0.960008 0
|
||||
18 0.957203 1.8445e-05
|
||||
31 104.52 0.00168382
|
||||
300 291.52794 -5216.2881 -6389.1342 1172.846 -6503.1276 27.889153 2.248246
|
||||
colvars: Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.584942 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 29.541 ns/day, 0.812 hours/ns, 170.957 timesteps/s
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.41044 | 0.41882 | 0.42773 | 1.1 | 71.60
|
||||
Bond | 0.00056911 | 0.0011486 | 0.0018017 | 1.4 | 0.20
|
||||
Kspace | 0.056211 | 0.064277 | 0.072168 | 2.7 | 10.99
|
||||
Neigh | 0.064606 | 0.064613 | 0.064617 | 0.0 | 11.05
|
||||
Comm | 0.013311 | 0.013966 | 0.015175 | 0.6 | 2.39
|
||||
Output | 0.00027871 | 0.00051689 | 0.0012221 | 0.0 | 0.09
|
||||
Modify | 0.019776 | 0.0199 | 0.020015 | 0.1 | 3.40
|
||||
Other | | 0.001705 | | | 0.29
|
||||
|
||||
Nlocal: 501 ave 513 max 472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 6612.75 ave 6681 max 6561 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177038 ave 180136 max 170218 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.369
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:01
|
||||
@ -1,260 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars2":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46
|
||||
Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14
|
||||
Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72
|
||||
Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90
|
||||
Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62
|
||||
Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01
|
||||
Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08
|
||||
Other | | 0.001465 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:02
|
||||
@ -1,260 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
colvars: Creating proxy instance
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing the collective variables module, version 2018-11-16.
|
||||
colvars: Please cite Fiorin et al, Mol Phys 2013:
|
||||
colvars: https://doi.org/10.1080/00268976.2013.813594
|
||||
colvars: in any publication based on this calculation.
|
||||
colvars: SMP parallelism is available.
|
||||
colvars: Using LAMMPS interface, version 2018-08-29.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Reading new configuration from file "peptide.colvars2":
|
||||
colvars: # smp = on [default]
|
||||
colvars: # colvarsTrajFrequency = 1
|
||||
colvars: # colvarsRestartFrequency = 1000
|
||||
colvars: # scriptedColvarForces = off [default]
|
||||
colvars: # scriptingAfterBiases = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new collective variable.
|
||||
colvars: # name = "one"
|
||||
colvars: Initializing a new "distance" component.
|
||||
colvars: # name = "" [default]
|
||||
colvars: # componentCoeff = 1 [default]
|
||||
colvars: # componentExp = 1 [default]
|
||||
colvars: # period = 0 [default]
|
||||
colvars: # wrapAround = 0 [default]
|
||||
colvars: # forceNoPBC = off [default]
|
||||
colvars: # scalable = on [default]
|
||||
colvars: Initializing atom group "group1".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: Initializing atom group "group2".
|
||||
colvars: # name = "" [default]
|
||||
colvars: # centerReference = off [default]
|
||||
colvars: # rotateReference = off [default]
|
||||
colvars: # atomsOfGroup = "" [default]
|
||||
colvars: # indexGroup = "" [default]
|
||||
colvars: # psfSegID = [default]
|
||||
colvars: # atomsFile = "" [default]
|
||||
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
colvars: # enableForces = on [default]
|
||||
colvars: # enableFitGradients = on [default]
|
||||
colvars: # printAtomIDs = off [default]
|
||||
colvars: Atom group "group2" defined, 4 atoms initialized: total mass = 4, total charge = 0.
|
||||
colvars: # oneSiteSystemForce = off [default]
|
||||
colvars: # oneSiteTotalForce = off [default]
|
||||
colvars: All components initialized.
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # width = 1 [default]
|
||||
colvars: # lowerBoundary = 0 [default]
|
||||
colvars: # upperBoundary = 0 [default]
|
||||
colvars: # expandBoundaries = off [default]
|
||||
colvars: # extendedLagrangian = off [default]
|
||||
colvars: # outputValue = on [default]
|
||||
colvars: # outputVelocity = off [default]
|
||||
colvars: # outputTotalForce = off [default]
|
||||
colvars: # outputAppliedForce = off [default]
|
||||
colvars: # subtractAppliedForce = off [default]
|
||||
colvars: # runAve = off [default]
|
||||
colvars: # corrFunc = off [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Initializing a new "harmonic" instance.
|
||||
colvars: # name = "h_pot"
|
||||
colvars: # colvars = { one }
|
||||
colvars: # outputEnergy = off [default]
|
||||
colvars: # timeStepFactor = 1 [default]
|
||||
colvars: # writeTISamples = off [default]
|
||||
colvars: # writeTIPMF = off [default]
|
||||
colvars: # centers = { 10 }
|
||||
colvars: # targetCenters = { 10 } [default]
|
||||
colvars: # outputCenters = off [default]
|
||||
colvars: # forceConstant = 100
|
||||
colvars: # targetForceConstant = -1 [default]
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables biases initialized, 1 in total.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Collective variables module (re)initialized.
|
||||
colvars: ----------------------------------------------------------------------
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 4.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 4.
|
||||
colvars: The restart output state file will be "rest.colvars.state".
|
||||
colvars: The final output state file will be "peptide2.colvars.state".
|
||||
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
|
||||
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
|
||||
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
|
||||
colvars: Performing analysis.
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
colvars: Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.629325 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 27.458 ns/day, 0.874 hours/ns, 158.900 timesteps/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.4012 | 0.41532 | 0.42829 | 1.9 | 65.99
|
||||
Bond | 0.0005219 | 0.0011545 | 0.0018291 | 1.8 | 0.18
|
||||
Kspace | 0.059271 | 0.071301 | 0.084393 | 4.4 | 11.33
|
||||
Neigh | 0.10416 | 0.10419 | 0.10424 | 0.0 | 16.56
|
||||
Comm | 0.015643 | 0.016628 | 0.017256 | 0.5 | 2.64
|
||||
Output | 0.00025177 | 0.00033599 | 0.00058722 | 0.0 | 0.05
|
||||
Modify | 0.01912 | 0.019129 | 0.019141 | 0.0 | 3.04
|
||||
Other | | 0.001264 | | | 0.20
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
colvars: Resetting the Collective Variables module.
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -1,163 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 2.21146 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.814 ns/day, 3.071 hours/ns, 45.219 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.6195 | 1.6195 | 1.6195 | 0.0 | 73.23
|
||||
Bond | 0.0033534 | 0.0033534 | 0.0033534 | 0.0 | 0.15
|
||||
Kspace | 0.17464 | 0.17464 | 0.17464 | 0.0 | 7.90
|
||||
Neigh | 0.37337 | 0.37337 | 0.37337 | 0.0 | 16.88
|
||||
Comm | 0.013891 | 0.013891 | 0.013891 | 0.0 | 0.63
|
||||
Output | 0.00037336 | 0.00037336 | 0.00037336 | 0.0 | 0.02
|
||||
Modify | 0.024753 | 0.024753 | 0.024753 | 0.0 | 1.12
|
||||
Other | | 0.001613 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:02
|
||||
@ -1,163 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11098 8.97155e-05
|
||||
6 0.996996 1.00568e-05
|
||||
8 1.08 6.02345e-06
|
||||
10 1.111 1.84253e-05
|
||||
12 1.08 7.2713e-06
|
||||
14 0.959996 0
|
||||
18 0.957198 3.36079e-05
|
||||
31 104.52 0.0030599
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.620672 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 27.841 ns/day, 0.862 hours/ns, 161.116 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.4029 | 0.41752 | 0.4307 | 1.7 | 67.27
|
||||
Bond | 0.00054789 | 0.0011698 | 0.0018225 | 1.8 | 0.19
|
||||
Kspace | 0.055853 | 0.069798 | 0.083975 | 4.3 | 11.25
|
||||
Neigh | 0.096553 | 0.096622 | 0.096707 | 0.0 | 15.57
|
||||
Comm | 0.015383 | 0.016022 | 0.01632 | 0.3 | 2.58
|
||||
Output | 0.00033116 | 0.00057495 | 0.0012989 | 0.0 | 0.09
|
||||
Modify | 0.017549 | 0.017693 | 0.017826 | 0.1 | 2.85
|
||||
Other | | 0.001274 | | | 0.21
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.412
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
@ -1,158 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 2.2037 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 7.841 ns/day, 3.061 hours/ns, 45.378 timesteps/s
|
||||
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.5852 | 1.5852 | 1.5852 | 0.0 | 71.93
|
||||
Bond | 0.0032725 | 0.0032725 | 0.0032725 | 0.0 | 0.15
|
||||
Kspace | 0.17308 | 0.17308 | 0.17308 | 0.0 | 7.85
|
||||
Neigh | 0.4027 | 0.4027 | 0.4027 | 0.0 | 18.27
|
||||
Comm | 0.014041 | 0.014041 | 0.014041 | 0.0 | 0.64
|
||||
Output | 0.00032306 | 0.00032306 | 0.00032306 | 0.0 | 0.01
|
||||
Modify | 0.023546 | 0.023546 | 0.023546 | 0.0 | 1.07
|
||||
Other | | 0.001546 | | | 0.07
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:02
|
||||
@ -1,158 +0,0 @@
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 5 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.11096 0.000191462
|
||||
6 0.996989 3.55508e-05
|
||||
8 1.08 9.0997e-06
|
||||
10 1.111 1.58544e-05
|
||||
12 1.08 5.80604e-06
|
||||
14 0.959997 0
|
||||
18 0.957198 2.92445e-05
|
||||
31 104.52 0.00239923
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.616036 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 28.050 ns/day, 0.856 hours/ns, 162.328 timesteps/s
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.40372 | 0.41244 | 0.41714 | 0.8 | 66.95
|
||||
Bond | 0.00053573 | 0.0011384 | 0.0017946 | 1.8 | 0.18
|
||||
Kspace | 0.060087 | 0.063993 | 0.07306 | 2.1 | 10.39
|
||||
Neigh | 0.1033 | 0.10349 | 0.1036 | 0.0 | 16.80
|
||||
Comm | 0.01568 | 0.016453 | 0.017178 | 0.5 | 2.67
|
||||
Output | 0.00028253 | 0.00032026 | 0.00043178 | 0.0 | 0.05
|
||||
Modify | 0.016238 | 0.016955 | 0.017704 | 0.5 | 2.75
|
||||
Other | | 0.001239 | | | 0.20
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Normal file
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.1
Normal file
@ -0,0 +1,732 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 5 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
The final output state file will be "out.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.897199 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.260 ns/day, 1.246 hours/ns, 111.458 timesteps/s, 223.362 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71298 | 0.71298 | 0.71298 | 0.0 | 79.47
|
||||
Bond | 0.001284 | 0.001284 | 0.001284 | 0.0 | 0.14
|
||||
Kspace | 0.041232 | 0.041232 | 0.041232 | 0.0 | 4.60
|
||||
Neigh | 0.1277 | 0.1277 | 0.1277 | 0.0 | 14.23
|
||||
Comm | 0.0033285 | 0.0033285 | 0.0033285 | 0.0 | 0.37
|
||||
Output | 0.00017467 | 0.00017467 | 0.00017467 | 0.0 | 0.02
|
||||
Modify | 0.010003 | 0.010003 | 0.010003 | 0.0 | 1.11
|
||||
Other | | 0.0004941 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Current simulation parameters: initial step = 100, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
|
||||
140 253.85111 -5452.1838 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7817 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1372 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4236 26.200127 3.4336037
|
||||
190 250.80862 -5555.2554 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.855092 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 20.208 ns/day, 1.188 hours/ns, 116.946 timesteps/s, 234.361 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71954 | 0.71954 | 0.71954 | 0.0 | 84.15
|
||||
Bond | 0.0012655 | 0.0012655 | 0.0012655 | 0.0 | 0.15
|
||||
Kspace | 0.042826 | 0.042826 | 0.042826 | 0.0 | 5.01
|
||||
Neigh | 0.078128 | 0.078128 | 0.078128 | 0.0 | 9.14
|
||||
Comm | 0.0029003 | 0.0029003 | 0.0029003 | 0.0 | 0.34
|
||||
Output | 0.00016605 | 0.00016605 | 0.00016605 | 0.0 | 0.02
|
||||
Modify | 0.0097753 | 0.0097753 | 0.0097753 | 0.0 | 1.14
|
||||
Other | | 0.0004882 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11159 ave 11159 max 11159 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708083 ave 708083 max 708083 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.33483
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
Setting initial step number from MD engine: 200
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 200, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
----------------------------------------------------------------------
|
||||
Loading state from text file "out.colvars.state".
|
||||
Restarting collective variable "one" from value: 10.0128
|
||||
Restarting collective variable "two" from value: 9.62236
|
||||
Restarted harmonic bias "h_pot" with step number 200.
|
||||
----------------------------------------------------------------------
|
||||
The final output state file will be "out2.colvars.state".
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4251 -6569.2538 1011.8288 -6674.0845 24.804906 7.1387572
|
||||
210 253.15302 -5538.5614 -6557.0213 1018.4599 -6672.0496 37.676621 0.61219488
|
||||
220 245.19621 -5522.5192 -6508.9681 986.44887 -6628.19 36.657688 0.048643387
|
||||
230 258.69885 -5495.7277 -6536.499 1040.7713 -6658.2888 34.857911 0.2209256
|
||||
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.1799 31.576952 3.7574815
|
||||
250 269.07527 -5438.3947 -6520.9114 1082.5167 -6616.4383 25.447674 8.6600023
|
||||
260 266.01046 -5397.3484 -6467.5351 1070.1867 -6580.2895 26.871919 8.3323102
|
||||
270 272.81307 -5350.882 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
|
||||
280 279.42264 -5307.9798 -6432.125 1124.1452 -6557.3367 33.644021 8.5490492
|
||||
290 286.85168 -5260.8411 -6414.874 1154.033 -6515.6797 28.574838 5.9100104
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.111 1.79793e-05 9
|
||||
Bond: 6 0.997005 1.02512e-05 6
|
||||
Bond: 8 1.08 1.85103e-05 7
|
||||
Bond: 10 1.111 9.9884e-06 8
|
||||
Bond: 12 1.08 8.84114e-06 9
|
||||
Bond: 14 0.960008 0 1
|
||||
Bond: 18 0.957203 1.8445e-05 1280
|
||||
Angle: 31 104.52 0.00168383 640
|
||||
300 291.52794 -5216.288 -6389.1341 1172.846 -6503.1276 27.889149 2.2482427
|
||||
Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.86889 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.887 ns/day, 1.207 hours/ns, 115.089 timesteps/s, 230.639 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.72728 | 0.72728 | 0.72728 | 0.0 | 83.70
|
||||
Bond | 0.0012755 | 0.0012755 | 0.0012755 | 0.0 | 0.15
|
||||
Kspace | 0.041631 | 0.041631 | 0.041631 | 0.0 | 4.79
|
||||
Neigh | 0.085283 | 0.085283 | 0.085283 | 0.0 | 9.82
|
||||
Comm | 0.0029986 | 0.0029986 | 0.0029986 | 0.0 | 0.35
|
||||
Output | 0.00013272 | 0.00013272 | 0.00013272 | 0.0 | 0.02
|
||||
Modify | 0.0097972 | 0.0097972 | 0.0097972 | 0.0 | 1.13
|
||||
Other | | 0.0004882 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11296 ave 11296 max 11296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708152 ave 708152 max 708152 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.36926
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:02
|
||||
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4
Normal file
732
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars.g++.4
Normal file
@ -0,0 +1,732 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f out*.colvars.*"
|
||||
fix 2 all colvars peptide.colvars
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 5 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
The final output state file will be "out.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "out.colvars.traj".
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.246405 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 70.128 ns/day, 0.342 hours/ns, 405.836 timesteps/s, 813.295 katom-step/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17765 | 0.18092 | 0.18373 | 0.6 | 73.42
|
||||
Bond | 0.00021581 | 0.00045219 | 0.00069916 | 0.0 | 0.18
|
||||
Kspace | 0.018035 | 0.020459 | 0.023812 | 1.7 | 8.30
|
||||
Neigh | 0.032165 | 0.032193 | 0.032207 | 0.0 | 13.07
|
||||
Comm | 0.00566 | 0.0058533 | 0.0060088 | 0.2 | 2.38
|
||||
Output | 0.00012205 | 0.00014069 | 0.00019404 | 0.0 | 0.06
|
||||
Modify | 0.0059979 | 0.0060225 | 0.0060368 | 0.0 | 2.44
|
||||
Other | | 0.0003631 | | | 0.15
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Current simulation parameters: initial step = 100, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
110 266.26438 -5341.1991 -6412.4073 1071.2082 -6552.7551 33.573173 1.9229657
|
||||
120 262.66604 -5386.2387 -6442.9704 1056.7317 -6587.5483 29.859587 2.7124812
|
||||
130 252.83379 -5422.5401 -6439.7157 1017.1756 -6580.4703 25.979343 1.2031591
|
||||
140 253.85111 -5452.1837 -6473.4521 1021.2684 -6609.4826 26.071651 0.30585517
|
||||
150 261.31816 -5490.4726 -6541.7816 1051.3091 -6646.6075 16.258823 6.9051008
|
||||
160 255.7352 -5521.5941 -6550.4423 1028.8483 -6658.1373 19.717399 12.339679
|
||||
170 253.42527 -5540.0942 -6559.6494 1019.5552 -6656.6678 23.293812 10.290217
|
||||
180 248.51161 -5550.3254 -6550.1125 999.78704 -6661.4235 26.200127 3.4336036
|
||||
190 250.80862 -5555.2555 -6564.2836 1009.0281 -6666.164 25.53634 3.3494286
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
|
||||
Saving collective variables state to "out.colvars.state".
|
||||
Loop time of 0.238087 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 72.578 ns/day, 0.331 hours/ns, 420.014 timesteps/s, 841.709 katom-step/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17913 | 0.18408 | 0.19082 | 1.1 | 77.32
|
||||
Bond | 0.00019617 | 0.00044139 | 0.00071286 | 0.0 | 0.19
|
||||
Kspace | 0.016186 | 0.022449 | 0.02737 | 3.0 | 9.43
|
||||
Neigh | 0.018728 | 0.018753 | 0.018777 | 0.0 | 7.88
|
||||
Comm | 0.0052171 | 0.0055397 | 0.0058422 | 0.3 | 2.33
|
||||
Output | 0.00012326 | 0.00014453 | 0.00020506 | 0.0 | 0.06
|
||||
Modify | 0.0062505 | 0.0062725 | 0.0062944 | 0.0 | 2.63
|
||||
Other | | 0.0004069 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 481 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 6556.5 ave 6608 max 6514 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 177021 ave 182259 max 172089 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 708083
|
||||
Ave neighs/atom = 353.33483
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 2 all colvars peptide.colvars input out.colvars.state output out2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
Setting initial step number from MD engine: 200
|
||||
|
||||
run 100
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Will read input state from file "out.colvars.state"----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "two"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 1 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 2 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one, two }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10, 10 }
|
||||
# targetCenters = { 10, 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
The force constant for colvar "two" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 200, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
Re-initialized atom group for variable "two":0/0. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
Re-initialized atom group for variable "two":0/1. 1 atoms: total mass = 12.011, total charge = 0.51.
|
||||
----------------------------------------------------------------------
|
||||
Loading state from text file "out.colvars.state".
|
||||
Restarting collective variable "one" from value: 10.0128
|
||||
Restarting collective variable "two" from value: 9.62236
|
||||
Restarted harmonic bias "h_pot" with step number 200.
|
||||
----------------------------------------------------------------------
|
||||
The final output state file will be "out2.colvars.state".
|
||||
SHAKE stats (type/ave/delta/count) on step 200
|
||||
Bond: 4 1.111 1.81266e-06 9
|
||||
Bond: 6 0.997 7.79424e-07 6
|
||||
Bond: 8 1.08 1.08903e-06 7
|
||||
Bond: 10 1.111 2.96503e-07 8
|
||||
Bond: 12 1.08 4.69038e-07 9
|
||||
Bond: 14 0.960001 0 1
|
||||
Bond: 18 0.957201 3.76471e-06 1280
|
||||
Angle: 31 104.52 0.000411055 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
200 251.50475 -5557.4252 -6569.2539 1011.8288 -6674.0846 24.804906 7.1387572
|
||||
210 253.15302 -5538.5615 -6557.0215 1018.4599 -6672.0498 37.676621 0.61219488
|
||||
220 245.19621 -5522.5191 -6508.9679 986.44887 -6628.1899 36.657688 0.048643387
|
||||
230 258.69885 -5495.7275 -6536.4989 1040.7713 -6658.2886 34.857911 0.22092559
|
||||
240 260.79633 -5469.8678 -6519.0775 1049.2097 -6624.18 31.576952 3.7574815
|
||||
250 269.07527 -5438.3946 -6520.9113 1082.5167 -6616.4382 25.447675 8.6600023
|
||||
260 266.01046 -5397.3485 -6467.5352 1070.1867 -6580.2896 26.871919 8.3323104
|
||||
270 272.81307 -5350.8819 -6448.4362 1097.5543 -6563.8228 23.114196 10.973132
|
||||
280 279.42265 -5307.9799 -6432.1251 1124.1452 -6557.3368 33.644022 8.5490489
|
||||
290 286.85168 -5260.841 -6414.874 1154.033 -6515.6797 28.574838 5.9100102
|
||||
SHAKE stats (type/ave/delta/count) on step 300
|
||||
Bond: 4 1.111 1.79793e-05 9
|
||||
Bond: 6 0.997005 1.02512e-05 6
|
||||
Bond: 8 1.08 1.85103e-05 7
|
||||
Bond: 10 1.111 9.9884e-06 8
|
||||
Bond: 12 1.08 8.84114e-06 9
|
||||
Bond: 14 0.960008 0 1
|
||||
Bond: 18 0.957203 1.8445e-05 1280
|
||||
Angle: 31 104.52 0.00168383 640
|
||||
300 291.52793 -5216.288 -6389.1341 1172.846 -6503.1275 27.88915 2.2482428
|
||||
Saving collective variables state to "out2.colvars.state".
|
||||
Loop time of 0.245933 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 70.263 ns/day, 0.342 hours/ns, 406.614 timesteps/s, 814.854 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17862 | 0.18666 | 0.19126 | 1.2 | 75.90
|
||||
Bond | 0.00021974 | 0.00048505 | 0.00077708 | 0.0 | 0.20
|
||||
Kspace | 0.018338 | 0.02317 | 0.031148 | 3.4 | 9.42
|
||||
Neigh | 0.022128 | 0.022183 | 0.022222 | 0.0 | 9.02
|
||||
Comm | 0.0059137 | 0.0060593 | 0.0064247 | 0.3 | 2.46
|
||||
Output | 0.00014648 | 0.00015946 | 0.00019596 | 0.0 | 0.06
|
||||
Modify | 0.0067012 | 0.00674 | 0.0067814 | 0.0 | 2.74
|
||||
Other | | 0.0004738 | | | 0.19
|
||||
|
||||
Nlocal: 501 ave 513 max 472 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Nghost: 6612.75 ave 6681 max 6561 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 177038 ave 180136 max 170218 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 708152
|
||||
Ave neighs/atom = 353.36926
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 8
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1
Normal file
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.1
Normal file
@ -0,0 +1,344 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 5 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars2":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 4 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10 }
|
||||
# targetCenters = { 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
The final output state file will be "peptide2.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.907882 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.033 ns/day, 1.261 hours/ns, 110.146 timesteps/s, 220.734 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71563 | 0.71563 | 0.71563 | 0.0 | 78.82
|
||||
Bond | 0.0013267 | 0.0013267 | 0.0013267 | 0.0 | 0.15
|
||||
Kspace | 0.042157 | 0.042157 | 0.042157 | 0.0 | 4.64
|
||||
Neigh | 0.13452 | 0.13452 | 0.13452 | 0.0 | 14.82
|
||||
Comm | 0.0034995 | 0.0034995 | 0.0034995 | 0.0 | 0.39
|
||||
Output | 0.00014584 | 0.00014584 | 0.00014584 | 0.0 | 0.02
|
||||
Modify | 0.010115 | 0.010115 | 0.010115 | 0.0 | 1.11
|
||||
Other | | 0.0004888 | | | 0.05
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Total wall time: 0:00:00
|
||||
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4
Normal file
344
examples/PACKAGES/colvars/log.5Aug24.peptide-colvars2.g++.4
Normal file
@ -0,0 +1,344 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
shell "rm -f peptide2.colvars.*"
|
||||
fix 2 all colvars peptide.colvars2 output peptide2
|
||||
----------------------------------------------------------------------
|
||||
Initializing the collective variables module, version 2024-06-04.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
Please cite Fiorin et al, Mol Phys 2013:
|
||||
https://doi.org/10.1080/00268976.2013.813594
|
||||
as well as all other papers listed below for individual features used.
|
||||
This version was built with the C++11 standard or higher.
|
||||
Summary of compile-time features available in this build:
|
||||
- SMP parallelism: enabled (num. threads = 1)
|
||||
- Lepton custom functions: available
|
||||
- Tcl interpreter: not available
|
||||
Using LAMMPS interface, version "2024-07-05".
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.colvar2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_2
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 5 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
----------------------------------------------------------------------
|
||||
Reading new configuration from file "peptide.colvars2":
|
||||
# units = "" [default]
|
||||
# smp = on [default]
|
||||
# colvarsTrajFrequency = 1
|
||||
# colvarsRestartFrequency = 1000
|
||||
# scriptedColvarForces = off [default]
|
||||
# scriptingAfterBiases = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new collective variable.
|
||||
# name = "one"
|
||||
Initializing a new "distance" component.
|
||||
# name = "" [default]
|
||||
# componentCoeff = 1 [default]
|
||||
# componentExp = 1 [default]
|
||||
# period = 0 [default]
|
||||
# wrapAround = 0 [default]
|
||||
# forceNoPBC = off [default]
|
||||
# scalable = on [default]
|
||||
Initializing atom group "group1".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group1" defined with 4 atoms requested.
|
||||
Initializing atom group "group2".
|
||||
# name = "" [default]
|
||||
# centerToOrigin = off [default]
|
||||
# centerToReference = off [default]
|
||||
# rotateToReference = off [default]
|
||||
# atomsOfGroup = "" [default]
|
||||
# indexGroup = "" [default]
|
||||
# psfSegID = [default]
|
||||
# atomsFile = "" [default]
|
||||
# dummyAtom = ( 0 , 0 , 0 ) [default]
|
||||
# enableFitGradients = on [default]
|
||||
# printAtomIDs = off [default]
|
||||
Atom group "group2" defined with 4 atoms requested.
|
||||
# oneSiteSystemForce = off [default]
|
||||
# oneSiteTotalForce = off [default]
|
||||
All components initialized.
|
||||
# timeStepFactor = 1 [default]
|
||||
# width = 1 [default]
|
||||
# lowerBoundary = 0 [default]
|
||||
# upperBoundary = 1 [default]
|
||||
# hardLowerBoundary = on [default]
|
||||
# hardUpperBoundary = off [default]
|
||||
# expandBoundaries = off [default]
|
||||
# extendedLagrangian = off [default]
|
||||
# outputValue = on [default]
|
||||
# outputVelocity = off [default]
|
||||
# outputTotalForce = off [default]
|
||||
# outputAppliedForce = off [default]
|
||||
# subtractAppliedForce = off [default]
|
||||
# runAve = off [default]
|
||||
# corrFunc = off [default]
|
||||
----------------------------------------------------------------------
|
||||
Collective variables initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Initializing a new "harmonic" instance.
|
||||
# name = "h_pot"
|
||||
# colvars = { one }
|
||||
# stepZeroData = off [default]
|
||||
# outputEnergy = off [default]
|
||||
# outputFreq = 1000 [default]
|
||||
# timeStepFactor = 1 [default]
|
||||
# writeTISamples = off [default]
|
||||
# writeTIPMF = off [default]
|
||||
# centers = { 10 }
|
||||
# targetCenters = { 10 } [default]
|
||||
# outputCenters = off [default]
|
||||
# forceConstant = 100
|
||||
# decoupling = off [default]
|
||||
# targetForceConstant = -1 [default]
|
||||
The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
|
||||
----------------------------------------------------------------------
|
||||
Collective variables biases initialized, 1 in total.
|
||||
----------------------------------------------------------------------
|
||||
Collective variables module (re)initialized.
|
||||
----------------------------------------------------------------------
|
||||
Current simulation parameters: initial step = 0, integration timestep = 2
|
||||
Updating atomic parameters (masses, charges, etc).
|
||||
Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
|
||||
Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
|
||||
The final output state file will be "peptide2.colvars.state".
|
||||
Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_2
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Saving collective variables state to "peptide2.colvars.state".
|
||||
Loop time of 0.253421 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 68.187 ns/day, 0.352 hours/ns, 394.600 timesteps/s, 790.779 katom-step/s
|
||||
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.1771 | 0.18185 | 0.18625 | 0.8 | 71.76
|
||||
Bond | 0.00028771 | 0.00056007 | 0.00087366 | 0.0 | 0.22
|
||||
Kspace | 0.017434 | 0.021451 | 0.026345 | 2.4 | 8.46
|
||||
Neigh | 0.035481 | 0.035495 | 0.035512 | 0.0 | 14.01
|
||||
Comm | 0.0064003 | 0.0065098 | 0.0065994 | 0.1 | 2.57
|
||||
Output | 0.00012417 | 0.00013888 | 0.00018109 | 0.0 | 0.05
|
||||
Modify | 0.0069389 | 0.0069521 | 0.0069617 | 0.0 | 2.74
|
||||
Other | | 0.0004667 | | | 0.18
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Colvars module (Fiorin2013, plus other works listed for specific features)
|
||||
|
||||
|
||||
% Colvars module:
|
||||
% Colvars-LAMMPS interface:
|
||||
% Harmonic colvar bias implementation:
|
||||
% Optimal rotation via flexible fitting:
|
||||
% distance colvar component:
|
||||
|
||||
@article{Fiorin2013,
|
||||
author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
|
||||
title = {Using collective variables to drive molecular dynamics simulations},
|
||||
journal = {Mol. Phys.},
|
||||
year = {2013},
|
||||
volume = {111},
|
||||
number = {22-23},
|
||||
pages = {3345--3362},
|
||||
publisher = {Taylor & Francis},
|
||||
doi = {10.1080/00268976.2013.813594},
|
||||
url = {https://doi.org/10.1080/00268976.2013.813594}
|
||||
}
|
||||
|
||||
|
||||
% LAMMPS engine:
|
||||
|
||||
@article{Thompson2022,
|
||||
title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
|
||||
author = {Thompson, Aidan P. and Aktulga, H. Metin and Berger, Richard and Bolintineanu, Dan S. and Brown, W. Michael and Crozier, Paul S. and {in't Veld}, Pieter J. and Kohlmeyer, Axel and Moore, Stan G. and Nguyen, Trung Dac and Shan, Ray and Stevens, Mark J. and Tranchida, Julien and Trott, Christian and Plimpton, Steven J.},
|
||||
journal = {Comp. Phys. Comm.},
|
||||
volume = {271},
|
||||
pages = {108171},
|
||||
year = {2022},
|
||||
doi = {10.1016/j.cpc.2021.108171},
|
||||
url = {https://doi.org/10.1016/j.cpc.2021.108171}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Total wall time: 0:00:00
|
||||
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1
Normal file
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.1
Normal file
@ -0,0 +1,194 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 5 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.893963 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 19.330 ns/day, 1.242 hours/ns, 111.861 timesteps/s, 224.170 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.7114 | 0.7114 | 0.7114 | 0.0 | 79.58
|
||||
Bond | 0.0012663 | 0.0012663 | 0.0012663 | 0.0 | 0.14
|
||||
Kspace | 0.041962 | 0.041962 | 0.041962 | 0.0 | 4.69
|
||||
Neigh | 0.12542 | 0.12542 | 0.12542 | 0.0 | 14.03
|
||||
Comm | 0.0033466 | 0.0033466 | 0.0033466 | 0.0 | 0.37
|
||||
Output | 0.00017765 | 0.00017765 | 0.00017765 | 0.0 | 0.02
|
||||
Modify | 0.0098927 | 0.0098927 | 0.0098927 | 0.0 | 1.11
|
||||
Other | | 0.0005014 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11124 ave 11124 max 11124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708237 ave 708237 max 708237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4
Normal file
194
examples/PACKAGES/colvars/log.5Aug24.peptide-spring.g++.4
Normal file
@ -0,0 +1,194 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.010 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 2a ref setforce 0.0 0.0 0.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
variable sp equal f_3a+f_3b
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond v_sp
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 5 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
|
||||
10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
|
||||
20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
|
||||
30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
|
||||
40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
|
||||
50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
|
||||
60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
|
||||
70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
|
||||
80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
|
||||
90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11098 8.97155e-05 9
|
||||
Bond: 6 0.996996 1.00568e-05 6
|
||||
Bond: 8 1.08 6.02345e-06 7
|
||||
Bond: 10 1.111 1.84253e-05 8
|
||||
Bond: 12 1.08 7.2713e-06 9
|
||||
Bond: 14 0.959996 0 1
|
||||
Bond: 18 0.957198 3.36079e-05 1280
|
||||
Angle: 31 104.52 0.0030599 640
|
||||
100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
|
||||
Loop time of 0.247541 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 69.806 ns/day, 0.344 hours/ns, 403.973 timesteps/s, 809.561 katom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17778 | 0.18129 | 0.18529 | 0.8 | 73.24
|
||||
Bond | 0.00024025 | 0.00049912 | 0.00080235 | 0.0 | 0.20
|
||||
Kspace | 0.016204 | 0.0204 | 0.023648 | 2.3 | 8.24
|
||||
Neigh | 0.032425 | 0.032462 | 0.032496 | 0.0 | 13.11
|
||||
Comm | 0.0063955 | 0.0065509 | 0.0067449 | 0.2 | 2.65
|
||||
Output | 0.0001675 | 0.00018071 | 0.00021385 | 0.0 | 0.07
|
||||
Modify | 0.0057027 | 0.0057304 | 0.0057568 | 0.0 | 2.31
|
||||
Other | | 0.0004289 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 489 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 6563.25 ave 6596 max 6519 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177059 ave 181742 max 172942 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 708237
|
||||
Ave neighs/atom = 353.41168
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 2
|
||||
Total wall time: 0:00:00
|
||||
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1
Normal file
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.1
Normal file
@ -0,0 +1,189 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.012 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 5 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.910778 on 1 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 18.973 ns/day, 1.265 hours/ns, 109.796 timesteps/s, 220.032 katom-step/s
|
||||
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.71746 | 0.71746 | 0.71746 | 0.0 | 78.77
|
||||
Bond | 0.0012756 | 0.0012756 | 0.0012756 | 0.0 | 0.14
|
||||
Kspace | 0.042462 | 0.042462 | 0.042462 | 0.0 | 4.66
|
||||
Neigh | 0.13497 | 0.13497 | 0.13497 | 0.0 | 14.82
|
||||
Comm | 0.0036247 | 0.0036247 | 0.0036247 | 0.0 | 0.40
|
||||
Output | 0.00016145 | 0.00016145 | 0.00016145 | 0.0 | 0.02
|
||||
Modify | 0.010258 | 0.010258 | 0.010258 | 0.0 | 1.13
|
||||
Other | | 0.0005695 | | | 0.06
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11143 ave 11143 max 11143 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708234 ave 708234 max 708234 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4
Normal file
189
examples/PACKAGES/colvars/log.5Aug24.peptide-spring2.g++.4
Normal file
@ -0,0 +1,189 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
Reading data file ...
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.011 seconds
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
group one id 2 4 5 6
|
||||
4 atoms in group one
|
||||
group two id 80 82 83 84
|
||||
4 atoms in group two
|
||||
group ref id 37
|
||||
1 atoms in group ref
|
||||
group colvar union one two ref
|
||||
9 atoms in group colvar
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
|
||||
fix 3 one spring couple two 100.0 0.0 0.0 0.0 10.0
|
||||
|
||||
fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
Finding SHAKE clusters ...
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
find clusters CPU = 0.000 seconds
|
||||
|
||||
#dump 1 colvar custom 1 dump.spring2.lammpstrj id xu yu zu fx fy fz
|
||||
#dump_modify 1 sort id
|
||||
|
||||
thermo_style custom step temp etotal pe ke epair ebond f_3
|
||||
thermo 10
|
||||
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.26872465
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.022820853
|
||||
estimated relative force accuracy = 6.872432e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 5 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 12
|
||||
ghost atom cutoff = 12
|
||||
binsize = 6, bins = 5 5 5
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmm/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 4 1.111 1.44264e-05 9
|
||||
Bond: 6 0.996998 7.26967e-06 6
|
||||
Bond: 8 1.08 1.32536e-05 7
|
||||
Bond: 10 1.111 1.22749e-05 8
|
||||
Bond: 12 1.08 1.11767e-05 9
|
||||
Bond: 14 0.96 0 1
|
||||
Bond: 18 0.957206 4.37979e-05 1280
|
||||
Angle: 31 104.519 0.00396029 640
|
||||
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
|
||||
Step Temp TotEng PotEng KinEng E_pair E_bond f_3
|
||||
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323
|
||||
10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
|
||||
20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
|
||||
30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
|
||||
40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
|
||||
50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
|
||||
60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
|
||||
70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
|
||||
80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
|
||||
90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 4 1.11096 0.000191462 9
|
||||
Bond: 6 0.996989 3.55508e-05 6
|
||||
Bond: 8 1.08 9.0997e-06 7
|
||||
Bond: 10 1.111 1.58544e-05 8
|
||||
Bond: 12 1.08 5.80604e-06 9
|
||||
Bond: 14 0.959997 0 1
|
||||
Bond: 18 0.957198 2.92445e-05 1280
|
||||
Angle: 31 104.52 0.00239923 640
|
||||
100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
|
||||
Loop time of 0.248812 on 4 procs for 100 steps with 2004 atoms
|
||||
|
||||
Performance: 69.450 ns/day, 0.346 hours/ns, 401.910 timesteps/s, 805.428 katom-step/s
|
||||
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.17522 | 0.18002 | 0.18454 | 1.0 | 72.35
|
||||
Bond | 0.00020312 | 0.00044793 | 0.00074786 | 0.0 | 0.18
|
||||
Kspace | 0.016556 | 0.021002 | 0.026079 | 3.0 | 8.44
|
||||
Neigh | 0.035695 | 0.03571 | 0.03572 | 0.0 | 14.35
|
||||
Comm | 0.0057324 | 0.0058127 | 0.005874 | 0.1 | 2.34
|
||||
Output | 0.00013005 | 0.00013946 | 0.00016548 | 0.0 | 0.06
|
||||
Modify | 0.00526 | 0.0052645 | 0.005272 | 0.0 | 2.12
|
||||
Other | | 0.0004197 | | | 0.17
|
||||
|
||||
Nlocal: 501 ave 513 max 494 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 6572.5 ave 6593 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Neighs: 177058 ave 181778 max 174301 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 708234
|
||||
Ave neighs/atom = 353.41018
|
||||
Ave special neighs/atom = 2.3403194
|
||||
Neighbor list builds = 13
|
||||
Dangerous builds = 1
|
||||
Total wall time: 0:00:00
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 200
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00127732034965e+01
|
||||
x 10.012773203962
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.62235997490241e+00
|
||||
x 9.6223599748448
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00136989326255e+01
|
||||
x 10.013698932648
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 1.00648830006091e+01
|
||||
x 10.064883000604
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -13,191 +13,191 @@
|
||||
11 1.01744058364969e+01 8.66916428851601e+00
|
||||
12 1.01894584969823e+01 8.75011341291751e+00
|
||||
13 1.02015949657517e+01 8.81261373358815e+00
|
||||
14 1.02107634786499e+01 8.86010572643564e+00
|
||||
14 1.02107634786498e+01 8.86010572643564e+00
|
||||
15 1.02172802335367e+01 8.89996164389908e+00
|
||||
16 1.02217586687617e+01 8.94046117354318e+00
|
||||
17 1.02249400729821e+01 8.98764357480963e+00
|
||||
18 1.02274821194763e+01 9.04385418276306e+00
|
||||
19 1.02297694921722e+01 9.10767828090644e+00
|
||||
20 1.02317948794015e+01 9.17521818721732e+00
|
||||
20 1.02317948794015e+01 9.17521818721733e+00
|
||||
21 1.02331324174422e+01 9.24256921345538e+00
|
||||
22 1.02330115052436e+01 9.30670040650459e+00
|
||||
22 1.02330115052436e+01 9.30670040650458e+00
|
||||
23 1.02304888847637e+01 9.36477739916766e+00
|
||||
24 1.02246905091409e+01 9.41471338314027e+00
|
||||
25 1.02150557312054e+01 9.45578119421866e+00
|
||||
26 1.02015018849614e+01 9.48855148434622e+00
|
||||
27 1.01844563445019e+01 9.51414398880334e+00
|
||||
26 1.02015018849613e+01 9.48855148434622e+00
|
||||
27 1.01844563445019e+01 9.51414398880333e+00
|
||||
28 1.01647618536435e+01 9.53348342780342e+00
|
||||
29 1.01435075836914e+01 9.54736918677922e+00
|
||||
30 1.01218448127414e+01 9.55679294480281e+00
|
||||
30 1.01218448127414e+01 9.55679294480282e+00
|
||||
31 1.01008234685872e+01 9.56289707955055e+00
|
||||
32 1.00812605992407e+01 9.56689852729787e+00
|
||||
33 1.00636482078211e+01 9.57008522470066e+00
|
||||
34 1.00481219532447e+01 9.57404682801174e+00
|
||||
35 1.00345149123742e+01 9.58097344406653e+00
|
||||
32 1.00812605992407e+01 9.56689852729789e+00
|
||||
33 1.00636482078211e+01 9.57008522470067e+00
|
||||
34 1.00481219532447e+01 9.57404682801176e+00
|
||||
35 1.00345149123742e+01 9.58097344406654e+00
|
||||
36 1.00224896192326e+01 9.59352147402459e+00
|
||||
37 1.00117065902086e+01 9.61412496221624e+00
|
||||
38 1.00019625883763e+01 9.64369256665448e+00
|
||||
39 9.99324045988116e+00 9.68100279483232e+00
|
||||
40 9.98566198277188e+00 9.72340741886406e+00
|
||||
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141 1.00644400705403e+01 9.95041823460627e+00
|
||||
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|
||||
143 1.00436834568360e+01 9.89050941892251e+00
|
||||
144 1.00330649755670e+01 9.85603943369589e+00
|
||||
145 1.00223855041248e+01 9.81818968320503e+00
|
||||
146 1.00118066120332e+01 9.77759398937178e+00
|
||||
147 1.00015635424482e+01 9.73590632987673e+00
|
||||
148 9.99195808450856e+00 9.69551862651774e+00
|
||||
149 9.98332973840472e+00 9.65911623099469e+00
|
||||
150 9.97599905822999e+00 9.62915505892649e+00
|
||||
151 9.97019367845638e+00 9.60716909703526e+00
|
||||
152 9.96598267372795e+00 9.59318709218540e+00
|
||||
153 9.96324606044969e+00 9.58559881066392e+00
|
||||
154 9.96169276237047e+00 9.58153758575953e+00
|
||||
155 9.96092625152242e+00 9.57763829328116e+00
|
||||
156 9.96054315740228e+00 9.57093750810941e+00
|
||||
157 9.96023482376251e+00 9.55965895382487e+00
|
||||
158 9.95985352333786e+00 9.54367776304373e+00
|
||||
159 9.95942460236116e+00 9.52452561453112e+00
|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
199 1.00122066751424e+01 9.63383866285097e+00
|
||||
200 1.00127732039621e+01 9.62235997484479e+00
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
configuration {
|
||||
step 300
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 9.95315918568411e+00
|
||||
x 9.9531592295885
|
||||
}
|
||||
|
||||
colvar {
|
||||
name two
|
||||
x 9.79318883680258e+00
|
||||
x 9.7931889789213
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -1,102 +1,102 @@
|
||||
# step one two
|
||||
200 1.00127732034965e+01 9.62235997490241e+00
|
||||
201 1.00139198864982e+01 9.61766167925624e+00
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
241 1.00548770491533e+01 9.72611599020063e+00
|
||||
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|
||||
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|
||||
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|
||||
245 1.00788811512303e+01 9.69472082245661e+00
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
295 1.00056261321876e+01 9.72399810930261e+00
|
||||
296 9.99406221883501e+00 9.74140402524052e+00
|
||||
297 9.98250803362175e+00 9.75776438941627e+00
|
||||
298 9.97160202027972e+00 9.77203069297329e+00
|
||||
299 9.96175637151037e+00 9.78379375044905e+00
|
||||
300 9.95315918568411e+00 9.79318883680258e+00
|
||||
200 1.00127732039621e+01 9.62235997484479e+00
|
||||
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|
||||
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|
||||
203 1.00172741984288e+01 9.63964899413135e+00
|
||||
204 1.00189052034286e+01 9.66786718668113e+00
|
||||
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|
||||
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|
||||
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|
||||
208 1.00162005542527e+01 9.83091553193592e+00
|
||||
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|
||||
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|
||||
211 1.00009200570685e+01 9.90798080630807e+00
|
||||
212 9.99531475670037e+00 9.92127385350745e+00
|
||||
213 9.99063399978946e+00 9.93157198491364e+00
|
||||
214 9.98737188290188e+00 9.94051482558046e+00
|
||||
215 9.98567126870035e+00 9.94885527853167e+00
|
||||
216 9.98528703143402e+00 9.95646746044078e+00
|
||||
217 9.98565831825084e+00 9.96275739920543e+00
|
||||
218 9.98606722850532e+00 9.96730423316541e+00
|
||||
219 9.98583581006681e+00 9.97036378874527e+00
|
||||
220 9.98450999905139e+00 9.97292736402649e+00
|
||||
221 9.98198432974296e+00 9.97627440161597e+00
|
||||
222 9.97853676608100e+00 9.98127101043889e+00
|
||||
223 9.97475981847134e+00 9.98785371579891e+00
|
||||
224 9.97140283904510e+00 9.99492286559338e+00
|
||||
225 9.96917134637541e+00 1.00005443234936e+01
|
||||
226 9.96854520536988e+00 1.00023222900809e+01
|
||||
227 9.96967372102824e+00 9.99790272698630e+00
|
||||
228 9.97237632329275e+00 9.98555959429830e+00
|
||||
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|
||||
230 9.98078771543058e+00 9.93636510426670e+00
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
239 1.00373944894039e+01 9.73349214878674e+00
|
||||
240 1.00463193546284e+01 9.72980720512224e+00
|
||||
241 1.00548769529672e+01 9.72611598750665e+00
|
||||
242 1.00626420263492e+01 9.72152571786963e+00
|
||||
243 1.00693108979996e+01 9.71531422666390e+00
|
||||
244 1.00747299927796e+01 9.70668631833486e+00
|
||||
245 1.00788810840328e+01 9.69472081315003e+00
|
||||
246 1.00818281015229e+01 9.67872528846535e+00
|
||||
247 1.00836382438846e+01 9.65899114629446e+00
|
||||
248 1.00843077202414e+01 9.63702965268533e+00
|
||||
249 1.00837304312378e+01 9.61431309843794e+00
|
||||
250 1.00817369677632e+01 9.59193246490958e+00
|
||||
251 1.00781951275561e+01 9.57162231665577e+00
|
||||
252 1.00731274389447e+01 9.55557271498134e+00
|
||||
253 1.00667870699195e+01 9.54559998431332e+00
|
||||
254 1.00596599010604e+01 9.54253145213164e+00
|
||||
255 1.00523957143832e+01 9.54593690642836e+00
|
||||
256 1.00457028598538e+01 9.55423080384305e+00
|
||||
257 1.00402419064054e+01 9.56514760196478e+00
|
||||
258 1.00365398159221e+01 9.57641295373454e+00
|
||||
259 1.00349276804438e+01 9.58620622717253e+00
|
||||
260 1.00355020510841e+01 9.59332345585722e+00
|
||||
261 1.00381137733017e+01 9.59732187421620e+00
|
||||
262 1.00423906427137e+01 9.59837617102817e+00
|
||||
263 1.00477959872900e+01 9.59679323453788e+00
|
||||
264 1.00537068694862e+01 9.59269522224878e+00
|
||||
265 1.00594937939774e+01 9.58610119961332e+00
|
||||
266 1.00645871442695e+01 9.57722116190429e+00
|
||||
267 1.00685317208695e+01 9.56668493059359e+00
|
||||
268 1.00710358435525e+01 9.55556250017823e+00
|
||||
269 1.00720144628669e+01 9.54520977349603e+00
|
||||
270 1.00716145056864e+01 9.53703780013997e+00
|
||||
271 1.00701992741473e+01 9.53227488069496e+00
|
||||
272 1.00682809229059e+01 9.53173332532930e+00
|
||||
273 1.00663988579612e+01 9.53554942356440e+00
|
||||
274 1.00649733547668e+01 9.54299861430164e+00
|
||||
275 1.00641836945973e+01 9.55262143202964e+00
|
||||
276 1.00639179095174e+01 9.56271517715327e+00
|
||||
277 1.00638154316074e+01 9.57192148613520e+00
|
||||
278 1.00633854335686e+01 9.57957875400668e+00
|
||||
279 1.00621627016565e+01 9.58572327370357e+00
|
||||
280 1.00598571070638e+01 9.59085686592320e+00
|
||||
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|
||||
282 1.00522576689401e+01 9.60085551333600e+00
|
||||
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|
||||
284 1.00437767554115e+01 9.61396710318380e+00
|
||||
285 1.00407546608873e+01 9.62178121653831e+00
|
||||
286 1.00390772967935e+01 9.62975551670189e+00
|
||||
287 1.00386905666453e+01 9.63733600598964e+00
|
||||
288 1.00391292301728e+01 9.64435235461356e+00
|
||||
289 1.00396076684883e+01 9.65114132457984e+00
|
||||
290 1.00391967232973e+01 9.65843914091158e+00
|
||||
291 1.00370408787737e+01 9.66713746391752e+00
|
||||
292 1.00325613002434e+01 9.67798048381559e+00
|
||||
293 1.00255913122523e+01 9.69130455064462e+00
|
||||
294 1.00164043783898e+01 9.70689857240811e+00
|
||||
295 1.00056261042358e+01 9.72399828398139e+00
|
||||
296 9.99406220236070e+00 9.74140420689973e+00
|
||||
297 9.98250803047048e+00 9.75776457125789e+00
|
||||
298 9.97160203186903e+00 9.77203086770013e+00
|
||||
299 9.96175639897897e+00 9.78379391142304e+00
|
||||
300 9.95315922958854e+00 9.79318897892133e+00
|
||||
|
||||
@ -1,12 +1,12 @@
|
||||
configuration {
|
||||
step 100
|
||||
dt 2.000000e+00
|
||||
version 2020-07-07
|
||||
version 2024-06-04
|
||||
}
|
||||
|
||||
colvar {
|
||||
name one
|
||||
x 1.00387423506482e+01
|
||||
x 10.038742350674
|
||||
}
|
||||
|
||||
restraint {
|
||||
|
||||
@ -20,16 +20,16 @@
|
||||
18 9.41602481112176e+00
|
||||
19 9.44413580740584e+00
|
||||
20 9.49001346044027e+00
|
||||
21 9.55036359015270e+00
|
||||
22 9.62258602486444e+00
|
||||
23 9.70460545744668e+00
|
||||
21 9.55036359015271e+00
|
||||
22 9.62258602486445e+00
|
||||
23 9.70460545744666e+00
|
||||
24 9.79475465622561e+00
|
||||
25 9.89135302429916e+00
|
||||
26 9.99213332770717e+00
|
||||
25 9.89135302429913e+00
|
||||
26 9.99213332770716e+00
|
||||
27 1.00938522423366e+01
|
||||
28 1.01925371414626e+01
|
||||
29 1.02845129002944e+01
|
||||
30 1.03676671987640e+01
|
||||
30 1.03676671987639e+01
|
||||
31 1.04416385355998e+01
|
||||
32 1.05071349561950e+01
|
||||
33 1.05650463398331e+01
|
||||
@ -41,39 +41,39 @@
|
||||
39 1.07331870068021e+01
|
||||
40 1.07158913924701e+01
|
||||
41 1.06789115566470e+01
|
||||
42 1.06198840652253e+01
|
||||
42 1.06198840652254e+01
|
||||
43 1.05380097743725e+01
|
||||
44 1.04346581978275e+01
|
||||
45 1.03132910149185e+01
|
||||
46 1.01792819503691e+01
|
||||
46 1.01792819503692e+01
|
||||
47 1.00398949454818e+01
|
||||
48 9.90373650268307e+00
|
||||
49 9.77934647164350e+00
|
||||
50 9.67343955381284e+00
|
||||
51 9.58957255517495e+00
|
||||
52 9.52771577288560e+00
|
||||
53 9.48463495848957e+00
|
||||
54 9.45495747488851e+00
|
||||
55 9.43277083061229e+00
|
||||
56 9.41329510571902e+00
|
||||
57 9.39417852043035e+00
|
||||
49 9.77934647164349e+00
|
||||
50 9.67343955381283e+00
|
||||
51 9.58957255517494e+00
|
||||
52 9.52771577288559e+00
|
||||
53 9.48463495848955e+00
|
||||
54 9.45495747488850e+00
|
||||
55 9.43277083061230e+00
|
||||
56 9.41329510571900e+00
|
||||
57 9.39417852043034e+00
|
||||
58 9.37607916767444e+00
|
||||
59 9.36243879601093e+00
|
||||
60 9.35853234890725e+00
|
||||
61 9.36993739187210e+00
|
||||
62 9.40084256925489e+00
|
||||
59 9.36243879601092e+00
|
||||
60 9.35853234890724e+00
|
||||
61 9.36993739187209e+00
|
||||
62 9.40084256925487e+00
|
||||
63 9.45286356660258e+00
|
||||
64 9.52464585631223e+00
|
||||
65 9.61230948096192e+00
|
||||
66 9.71074418990813e+00
|
||||
67 9.81507236552599e+00
|
||||
68 9.92117974657176e+00
|
||||
69 1.00244259961919e+01
|
||||
66 9.71074418990814e+00
|
||||
67 9.81507236552600e+00
|
||||
68 9.92117974657179e+00
|
||||
69 1.00244259961920e+01
|
||||
70 1.01178306268727e+01
|
||||
71 1.01986985644537e+01
|
||||
71 1.01986985644538e+01
|
||||
72 1.02671003889995e+01
|
||||
73 1.03213098011429e+01
|
||||
74 1.03597236984298e+01
|
||||
73 1.03213098011430e+01
|
||||
74 1.03597236984299e+01
|
||||
75 1.03817789163109e+01
|
||||
76 1.03880650963390e+01
|
||||
77 1.03809140245635e+01
|
||||
@ -82,21 +82,21 @@
|
||||
80 1.03243676495902e+01
|
||||
81 1.03082131278348e+01
|
||||
82 1.02961310659179e+01
|
||||
83 1.02862115513553e+01
|
||||
83 1.02862115513552e+01
|
||||
84 1.02756073299153e+01
|
||||
85 1.02618115461408e+01
|
||||
86 1.02435127550163e+01
|
||||
87 1.02212112849545e+01
|
||||
88 1.01972788307491e+01
|
||||
89 1.01743918261207e+01
|
||||
89 1.01743918261206e+01
|
||||
90 1.01538328424605e+01
|
||||
91 1.01363005552771e+01
|
||||
92 1.01223066231827e+01
|
||||
93 1.01118037967830e+01
|
||||
92 1.01223066231826e+01
|
||||
93 1.01118037967829e+01
|
||||
94 1.01038502876980e+01
|
||||
95 1.00967012947728e+01
|
||||
96 1.00885779123137e+01
|
||||
97 1.00784256309007e+01
|
||||
98 1.00661429612272e+01
|
||||
99 1.00524913461711e+01
|
||||
100 1.00387423506482e+01
|
||||
95 1.00967012947726e+01
|
||||
96 1.00885779123133e+01
|
||||
97 1.00784256308996e+01
|
||||
98 1.00661429612359e+01
|
||||
99 1.00524913461887e+01
|
||||
100 1.00387423506735e+01
|
||||
|
||||
340
examples/charmmfsw/charmmff.cmap
Normal file
340
examples/charmmfsw/charmmff.cmap
Normal file
@ -0,0 +1,340 @@
|
||||
#CMAP for C NH1 CT1 C NH1 CT1 C NH1; id=1
|
||||
#phi = -180.000000
|
||||
0.130000 0.770000 0.970000 1.250000 2.120000
|
||||
2.720000 2.090000 1.790000 0.780000 -0.690000
|
||||
1.000000 -2.200000 -4.830000 -4.820000 -4.910000
|
||||
-3.590000 -2.770000 -2.780000 -2.450000 -2.350000
|
||||
-2.340000 -1.520000 -0.950000 -0.040000
|
||||
|
||||
#phi = -165.000000
|
||||
-0.130000 1.380000 1.580000 1.870000 2.400000
|
||||
2.490000 2.440000 1.930000 1.090000 0.640000
|
||||
0.260000 -2.800000 -4.010000 -4.140000 -3.420000
|
||||
-2.600000 -2.300000 -1.500000 -1.100000 -0.860000
|
||||
-0.640000 -0.210000 -1.080000 -1.120000
|
||||
|
||||
#phi = -150.000000
|
||||
0.080000 1.420000 1.620000 2.050000 2.650000
|
||||
2.720000 2.320000 1.990000 1.560000 2.460000
|
||||
-0.230000 -1.820000 -2.580000 -3.010000 -2.550000
|
||||
-1.890000 -1.350000 -0.730000 0.070000 -0.230000
|
||||
-0.770000 -1.280000 -1.290000 -0.820000
|
||||
|
||||
#phi = -135.000000
|
||||
0.930000 1.520000 2.240000 2.550000 3.110000
|
||||
2.920000 2.460000 2.190000 2.060000 1.850000
|
||||
0.120000 -1.180000 -2.000000 -2.280000 -1.960000
|
||||
-1.340000 -0.930000 0.020000 0.310000 -0.520000
|
||||
-1.150000 -0.980000 -0.570000 -0.440000
|
||||
|
||||
#phi = -120.000000
|
||||
1.360000 1.960000 2.700000 3.040000 3.700000
|
||||
3.560000 2.640000 2.770000 2.720000 1.630000
|
||||
0.710000 -0.790000 -2.120000 -2.630000 -1.800000
|
||||
-0.430000 -0.060000 0.440000 0.910000 -0.550000
|
||||
-0.970000 -0.860000 -0.250000 0.450000
|
||||
|
||||
#phi = -105.000000
|
||||
2.050000 2.540000 2.820000 3.090000 3.370000
|
||||
3.550000 3.070000 2.900000 2.960000 2.120000
|
||||
0.910000 -0.820000 -2.090000 -2.240000 -1.460000
|
||||
0.210000 0.080000 0.770000 1.040000 -0.120000
|
||||
-0.320000 -0.160000 0.310000 0.730000
|
||||
|
||||
#phi = -90.000000
|
||||
1.450000 2.750000 2.740000 3.160000 3.450000
|
||||
3.340000 3.180000 3.900000 3.340000 2.440000
|
||||
0.910000 -0.610000 -1.510000 -1.620000 -0.960000
|
||||
-0.020000 0.420000 0.910000 0.460000 0.150000
|
||||
-0.070000 0.020000 0.280000 0.750000
|
||||
|
||||
#phi = -75.000000
|
||||
1.380000 3.350000 2.350000 3.060000 3.810000
|
||||
3.700000 3.580000 4.210000 3.540000 1.690000
|
||||
0.100000 -0.680000 -0.120000 -0.430000 -0.600000
|
||||
0.230000 0.420000 0.300000 0.550000 0.190000
|
||||
-0.250000 -0.190000 -0.250000 0.470000
|
||||
|
||||
#phi = -60.000000
|
||||
0.240000 1.230000 1.720000 3.170000 4.210000
|
||||
4.390000 4.280000 3.670000 2.270000 -0.480000
|
||||
-0.410000 -0.040000 -0.360000 -0.820000 -0.170000
|
||||
0.140000 0.270000 0.320000 0.310000 -0.670000
|
||||
-0.950000 -1.530000 -1.480000 -0.200000
|
||||
|
||||
#phi = -45.000000
|
||||
-1.180000 0.080000 2.350000 4.210000 5.380000
|
||||
5.390000 4.380000 2.460000 1.120000 0.110000
|
||||
0.010000 -0.150000 -0.800000 -0.580000 0.080000
|
||||
0.270000 -0.050000 0.380000 0.250000 -0.890000
|
||||
-1.580000 -1.950000 -1.980000 -2.000000
|
||||
|
||||
#phi = -30.000000
|
||||
-1.170000 1.070000 4.180000 6.740000 6.070000
|
||||
4.810000 2.780000 1.320000 0.770000 -0.010000
|
||||
0.280000 -0.710000 1.310000 1.520000 1.920000
|
||||
2.220000 0.190000 0.530000 0.330000 -1.600000
|
||||
-2.850000 -3.550000 -3.280000 -2.660000
|
||||
|
||||
#phi = -15.000000
|
||||
0.290000 5.590000 3.730000 3.220000 3.270000
|
||||
2.520000 1.590000 1.380000 0.860000 0.660000
|
||||
1.620000 0.850000 0.510000 0.740000 1.020000
|
||||
1.620000 -0.340000 0.180000 -0.610000 -2.560000
|
||||
-3.790000 -3.810000 -3.160000 -1.750000
|
||||
|
||||
#phi = 0.000000
|
||||
2.830000 0.790000 0.320000 0.480000 0.630000
|
||||
0.980000 1.240000 1.670000 1.650000 2.520000
|
||||
1.610000 0.780000 0.120000 0.070000 0.120000
|
||||
-1.570000 -1.210000 -1.930000 -2.600000 -3.790000
|
||||
-3.930000 -3.620000 -2.680000 -0.920000
|
||||
|
||||
#phi = 15.000000
|
||||
-0.780000 -1.910000 -2.050000 -1.850000 -1.050000
|
||||
0.180000 1.680000 2.220000 1.360000 2.450000
|
||||
1.440000 0.680000 -0.240000 -0.540000 -0.790000
|
||||
-2.180000 -3.210000 -4.350000 -3.940000 -3.910000
|
||||
-3.460000 -2.770000 1.760000 0.310000
|
||||
|
||||
#phi = 30.000000
|
||||
-2.960000 -3.480000 -3.440000 -2.400000 -1.130000
|
||||
0.340000 1.430000 1.390000 0.970000 2.460000
|
||||
1.520000 0.550000 -0.410000 -1.480000 -3.580000
|
||||
-4.130000 -4.560000 -4.440000 -3.580000 -2.960000
|
||||
-1.960000 -1.070000 -1.600000 -2.450000
|
||||
|
||||
#phi = 45.000000
|
||||
-4.020000 -3.840000 -3.370000 -2.330000 -0.980000
|
||||
0.360000 0.810000 0.750000 0.500000 1.900000
|
||||
0.770000 -0.420000 -3.290000 -3.910000 -4.520000
|
||||
-4.890000 -3.850000 -4.150000 -2.670000 -2.370000
|
||||
-2.860000 -3.420000 -3.670000 -3.600000
|
||||
|
||||
#phi = 60.000000
|
||||
-3.350000 -2.980000 -2.320000 -1.240000 -0.260000
|
||||
0.720000 0.670000 0.440000 2.400000 1.630000
|
||||
-2.010000 -3.310000 -3.990000 -4.530000 -4.850000
|
||||
-3.770000 -3.940000 -3.890000 -2.610000 -3.510000
|
||||
-3.760000 -3.640000 -3.450000 -3.340000
|
||||
|
||||
#phi = 75.000000
|
||||
-2.250000 -1.640000 -1.010000 0.040000 0.640000
|
||||
0.820000 0.520000 -0.010000 -0.370000 -1.190000
|
||||
-2.390000 -3.380000 -4.500000 -5.590000 -5.510000
|
||||
-4.940000 -3.830000 -3.840000 -3.700000 -4.150000
|
||||
-4.170000 -3.730000 -3.740000 -2.620000
|
||||
|
||||
#phi = 90.000000
|
||||
-1.720000 -1.180000 -0.430000 0.280000 0.810000
|
||||
0.800000 0.480000 -0.340000 -0.790000 -1.770000
|
||||
-2.810000 -3.800000 -5.220000 -6.280000 -6.580000
|
||||
-5.640000 -5.060000 -4.020000 -4.150000 -4.470000
|
||||
-4.100000 -3.770000 -3.160000 -2.650000
|
||||
|
||||
#phi = 105.000000
|
||||
-1.850000 -1.090000 -0.450000 0.130000 1.010000
|
||||
0.880000 0.490000 -0.220000 -0.860000 -1.680000
|
||||
-3.010000 -4.130000 -5.990000 -6.860000 -6.830000
|
||||
-5.850000 -3.860000 -4.860000 -4.910000 -4.720000
|
||||
-4.600000 -4.090000 -3.270000 -2.410000
|
||||
|
||||
#phi = 120.000000
|
||||
-1.970000 -1.120000 -0.540000 -0.150000 0.760000
|
||||
1.040000 0.760000 0.310000 -0.330000 -1.870000
|
||||
-3.370000 -5.010000 -6.120000 -7.050000 -6.980000
|
||||
-3.700000 -4.510000 -5.090000 -5.420000 -4.850000
|
||||
-4.440000 -4.000000 -3.420000 -2.750000
|
||||
|
||||
#phi = 135.000000
|
||||
-2.110000 -1.170000 -0.320000 -0.010000 0.320000
|
||||
1.090000 0.940000 0.630000 -0.170000 -1.830000
|
||||
-3.470000 -4.950000 -6.110000 -1.920000 -4.050000
|
||||
-5.000000 -5.000000 -4.840000 -4.890000 -4.300000
|
||||
-4.490000 -4.440000 -4.160000 -3.180000
|
||||
|
||||
#phi = 150.000000
|
||||
-1.760000 -0.400000 0.020000 0.360000 0.630000
|
||||
1.260000 1.360000 0.950000 -0.070000 -1.480000
|
||||
-3.150000 1.840000 -1.760000 -5.090000 -5.740000
|
||||
-5.390000 -4.780000 -4.190000 -4.120000 -4.040000
|
||||
-4.130000 -4.030000 -4.030000 -2.940000
|
||||
|
||||
#phi = 165.000000
|
||||
-0.810000 -0.070000 0.380000 0.540000 1.280000
|
||||
1.640000 1.700000 1.520000 0.630000 -1.090000
|
||||
-2.740000 -0.740000 -4.560000 -6.410000 -5.890000
|
||||
-5.140000 -4.190000 -3.670000 -3.840000 -3.560000
|
||||
-3.550000 -3.250000 -2.750000 -1.810000
|
||||
|
||||
|
||||
#CMAP for C NH1 CT2 C NH1 CT2 C NH1; id=2
|
||||
#phi = -180.000000
|
||||
0.235350 0.182300 0.177200 0.396800 0.859400
|
||||
1.489700 2.092500 2.297700 1.808600 0.696200
|
||||
-0.563300 -1.432700 -1.015100 1.426300 -0.564300
|
||||
0.696200 1.808200 2.301700 2.092600 1.489100
|
||||
0.859500 0.396900 0.176900 0.182400
|
||||
|
||||
#phi = -165.000000
|
||||
0.020100 -0.203800 -0.269700 0.014200 0.620800
|
||||
1.392400 2.046200 2.188200 1.683900 0.688500
|
||||
-0.373700 -0.703500 0.837800 3.704000 -0.730100
|
||||
0.594100 1.713100 2.205800 2.026400 1.529800
|
||||
1.027400 0.623800 0.348400 0.182800
|
||||
|
||||
#phi = -150.000000
|
||||
-0.533600 -0.807400 -0.804600 -0.379800 0.365300
|
||||
1.168000 1.641000 1.618100 1.302200 0.615100
|
||||
0.065700 0.738500 2.959500 -2.036600 -0.934600
|
||||
0.407900 1.517000 1.984800 1.833100 1.435200
|
||||
0.995600 0.562200 0.150600 -0.209000
|
||||
|
||||
#phi = -135.000000
|
||||
-1.208500 -1.429400 -1.319200 -0.817500 -0.112400
|
||||
0.454400 0.737600 0.879300 0.850100 0.670300
|
||||
0.943500 -2.651200 -2.829400 -2.199100 -1.065700
|
||||
0.279600 1.322000 1.668300 1.521300 1.193900
|
||||
0.765300 0.246000 -0.315500 -0.823200
|
||||
|
||||
#phi = -120.000000
|
||||
-1.789100 -1.965500 -1.860700 -1.447900 -0.896500
|
||||
-0.401000 -0.015100 0.321300 0.634600 0.976300
|
||||
-1.977500 -2.883200 -2.848500 -2.137900 -0.960300
|
||||
0.308700 1.098100 1.245300 1.133600 0.881800
|
||||
0.448200 -0.153900 -0.823700 -1.404300
|
||||
|
||||
#phi = -105.000000
|
||||
-2.246700 -2.487000 -2.473700 -2.135600 -1.577700
|
||||
-0.980600 -0.429100 0.144700 0.734000 -0.918300
|
||||
-2.299200 -2.882200 -2.668600 -1.847100 -0.719800
|
||||
0.107000 0.496000 0.553500 0.584300 0.494000
|
||||
0.098300 -0.529800 -1.237900 -1.840100
|
||||
|
||||
#phi = -90.000000
|
||||
-2.851100 -3.181100 -3.199500 -2.785300 -2.054300
|
||||
-1.242900 -0.476500 0.288100 -0.045300 -1.470600
|
||||
-2.558800 -2.869400 -2.450300 -1.582200 -0.930800
|
||||
-0.426400 -0.022700 0.000000 -0.097400 -0.136100
|
||||
-0.439600 -1.038600 -1.741000 -2.373200
|
||||
|
||||
#phi = -75.000000
|
||||
-3.961800 -4.268200 -4.109000 -3.364700 -2.252200
|
||||
-1.140400 -0.209800 0.487300 -0.746200 -2.127700
|
||||
-2.932100 -2.898500 -2.247900 -1.730400 -1.177200
|
||||
-0.448200 0.034900 -0.073300 -0.531600 -0.933300
|
||||
-1.360700 -2.009200 -2.745700 -3.424900
|
||||
|
||||
#phi = -60.000000
|
||||
-5.408000 -5.355100 -4.640100 -3.283200 -1.710200
|
||||
-0.423800 0.354400 -0.103700 -1.577700 -2.828300
|
||||
-3.151200 -2.649200 -2.183000 -1.761200 -0.981700
|
||||
-0.174700 0.262600 0.039200 -0.663000 -1.530700
|
||||
-2.478200 -3.465600 -4.334200 -5.011200
|
||||
|
||||
#phi = -45.000000
|
||||
-6.093200 -5.298400 -3.816620 -1.922530 -0.196160
|
||||
0.768200 0.568500 -0.831300 -2.343900 -3.037100
|
||||
-2.663700 -2.191100 -2.022900 -1.438500 -0.649000
|
||||
0.077000 0.441500 0.257500 -0.491100 -1.820600
|
||||
-3.473100 -4.895200 -5.790700 -6.205900
|
||||
|
||||
#phi = -30.000000
|
||||
-5.258225 -3.675795 -1.631110 0.430085 1.496470
|
||||
0.318200 -0.555100 -1.695500 -2.434200 -2.192600
|
||||
-1.691300 -1.890000 -1.708500 -1.206300 -0.567400
|
||||
0.054300 0.497200 0.599600 -0.171000 -2.137600
|
||||
-4.237000 -5.584100 -6.135100 -6.067000
|
||||
|
||||
#phi = -15.000000
|
||||
-3.161820 -0.902080 1.432450 -1.452885 -1.560780
|
||||
-1.665600 -1.783100 -1.755100 -1.329300 -0.731100
|
||||
-1.317000 -1.662800 -1.601200 -1.294900 -0.817300
|
||||
-0.197100 0.549500 0.850400 -0.689700 -2.819900
|
||||
-4.393000 -5.111500 -5.205690 -4.654785
|
||||
|
||||
#phi = 0.000000
|
||||
0.034035 -2.349860 -3.412065 -3.620070 -3.450950
|
||||
-2.875650 -1.787800 -0.541250 0.410450 -0.372500
|
||||
-1.126850 -1.498450 -1.608700 -1.498450 -1.126850
|
||||
-0.372500 0.410450 -0.541250 -1.787800 -2.875650
|
||||
-3.450950 -3.620070 -3.412065 -2.349860
|
||||
|
||||
#phi = 15.000000
|
||||
-3.162345 -4.654785 -5.205690 -5.111500 -4.393000
|
||||
-2.819900 -0.689700 0.850400 0.549500 -0.197100
|
||||
-0.817300 -1.294900 -1.601200 -1.662800 -1.317000
|
||||
-0.731100 -1.329300 -1.755100 -1.783100 -1.665600
|
||||
-1.560780 -1.452885 1.432450 -0.902080
|
||||
|
||||
#phi = 30.000000
|
||||
-5.258220 -6.067000 -6.135100 -5.584100 -4.237000
|
||||
-2.137600 -0.171000 0.599600 0.497200 0.054300
|
||||
-0.567400 -1.206300 -1.708500 -1.890000 -1.691300
|
||||
-2.192600 -2.434200 -1.695500 -0.555100 0.318200
|
||||
1.496470 0.430085 -1.631110 -3.675795
|
||||
|
||||
#phi = 45.000000
|
||||
-6.093300 -6.205900 -5.790700 -4.895200 -3.473100
|
||||
-1.820600 -0.491100 0.257500 0.441500 0.077000
|
||||
-0.649000 -1.438500 -2.022900 -2.191100 -2.663700
|
||||
-3.037100 -2.343900 -0.831300 0.568500 0.768200
|
||||
-0.196160 -1.922530 -3.816620 -5.298400
|
||||
|
||||
#phi = 60.000000
|
||||
-5.407500 -5.011200 -4.334200 -3.465600 -2.478200
|
||||
-1.530700 -0.663000 0.039200 0.262600 -0.174700
|
||||
-0.981700 -1.761200 -2.183000 -2.649200 -3.151200
|
||||
-2.828300 -1.577700 -0.103700 0.354400 -0.423800
|
||||
-1.710200 -3.283200 -4.640100 -5.355100
|
||||
|
||||
#phi = 75.000000
|
||||
-3.961900 -3.424900 -2.745700 -2.009200 -1.360700
|
||||
-0.933300 -0.531600 -0.073300 0.034900 -0.448200
|
||||
-1.177200 -1.730400 -2.247900 -2.898500 -2.932100
|
||||
-2.127700 -0.746200 0.487300 -0.209800 -1.140400
|
||||
-2.252200 -3.364700 -4.109000 -4.268200
|
||||
|
||||
#phi = 90.000000
|
||||
-2.854500 -2.373200 -1.741000 -1.038600 -0.439600
|
||||
-0.136100 -0.097400 0.000000 -0.022700 -0.426400
|
||||
-0.930800 -1.582200 -2.450300 -2.869400 -2.558800
|
||||
-1.470600 -0.045300 0.288100 -0.476500 -1.242900
|
||||
-2.054300 -2.785300 -3.199500 -3.181100
|
||||
|
||||
#phi = 105.000000
|
||||
-2.246400 -1.840100 -1.237900 -0.529800 0.098300
|
||||
0.494000 0.584300 0.553500 0.496000 0.107000
|
||||
-0.719800 -1.847100 -2.668600 -2.882200 -2.299200
|
||||
-0.918300 0.734000 0.144700 -0.429100 -0.980600
|
||||
-1.577700 -2.135600 -2.473700 -2.487000
|
||||
|
||||
#phi = 120.000000
|
||||
-1.788800 -1.404300 -0.823700 -0.153900 0.448200
|
||||
0.881800 1.133600 1.245300 1.098100 0.308700
|
||||
-0.960300 -2.137900 -2.848500 -2.883200 -1.977500
|
||||
0.976300 0.634600 0.321300 -0.015100 -0.401000
|
||||
-0.896500 -1.447900 -1.860700 -1.965500
|
||||
|
||||
#phi = 135.000000
|
||||
-1.208900 -0.823200 -0.315500 0.246000 0.765300
|
||||
1.193900 1.521300 1.668300 1.322000 0.279600
|
||||
-1.065700 -2.199100 -2.829400 -2.651200 0.943500
|
||||
0.670300 0.850100 0.879300 0.737600 0.454400
|
||||
-0.112400 -0.817500 -1.319200 -1.429400
|
||||
|
||||
#phi = 150.000000
|
||||
-0.533400 -0.209000 0.150600 0.562200 0.995600
|
||||
1.435200 1.833100 1.984800 1.517000 0.407900
|
||||
-0.934600 -2.036600 2.959500 0.738500 0.065700
|
||||
0.615100 1.302200 1.618100 1.641000 1.168000
|
||||
0.365300 -0.379800 -0.804600 -0.807400
|
||||
|
||||
#phi = 165.000000
|
||||
0.019900 0.182800 0.348400 0.623800 1.027400
|
||||
1.529800 2.026400 2.205800 1.713100 0.594100
|
||||
-0.730100 3.704000 0.837800 -0.703500 -0.373700
|
||||
0.688500 1.683900 2.188200 2.046200 1.392400
|
||||
0.620800 0.014200 -0.269700 -0.203800
|
||||
|
||||
|
||||
BIN
examples/charmmfsw/data.charmmfsw.gz
Normal file
BIN
examples/charmmfsw/data.charmmfsw.gz
Normal file
Binary file not shown.
46
examples/charmmfsw/in.charmmfsw
Normal file
46
examples/charmmfsw/in.charmmfsw
Normal file
@ -0,0 +1,46 @@
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
# for visualization with LAMMPS-GUI
|
||||
group water type 18 60
|
||||
group nowater subtract all water
|
||||
group ions type 63 64
|
||||
group other subtract all water ions
|
||||
|
||||
# dump viz other image 10 myimage-*.ppm element type size 800 800 zoom 2.82954 shiny 0.5 fsaa yes bond none none view 20 10 box no 0.0 axes no 0.0 0.0 center s 0.521318 0.489856 0.489856
|
||||
# dump_modify viz pad 9 boxcolor darkblue backcolor darkgray element H H H H H H H H H H H H H H H H H H C C C C C C C C C C C C C C C C C C C N N N N N N N N N N N N N N O O O O O O O O O P S Cl K adiam 1 1.92 adiam 2 1.92 adiam 3 1.92 adiam 4 1.92 adiam 5 1.92 adiam 6 1.92 adiam 7 1.92 adiam 8 1.92 adiam 9 1.92 adiam 10 1.92 adiam 11 1.92 adiam 12 1.92 adiam 13 1.92 adiam 14 1.92 adiam 15 1.92 adiam 16 1.92 adiam 17 1.92 adiam 18 1.92 adiam 19 2.72 adiam 20 2.72 adiam 21 2.72 adiam 22 2.72 adiam 23 2.72 adiam 24 2.72 adiam 25 2.72 adiam 26 2.72 adiam 27 2.72 adiam 28 2.72 adiam 29 2.72 adiam 30 2.72 adiam 31 2.72 adiam 32 2.72 adiam 33 2.72 adiam 34 2.72 adiam 35 2.72 adiam 36 2.72 adiam 37 2.72 adiam 38 2.48 adiam 39 2.48 adiam 40 2.48 adiam 41 2.48 adiam 42 2.48 adiam 43 2.48 adiam 44 2.48 adiam 45 2.48 adiam 46 2.48 adiam 47 2.48 adiam 48 2.48 adiam 49 2.48 adiam 50 2.48 adiam 51 2.48 adiam 52 2.432 adiam 53 2.432 adiam 54 2.432 adiam 55 2.432 adiam 56 2.432 adiam 57 2.432 adiam 58 2.432 adiam 59 2.432 adiam 60 2.432 adiam 61 2.88 adiam 62 2.88 adiam 63 3.632 adiam 64 2.816
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.1
Normal file
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.1
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
Reading CMAP parameters from: charmmff.cmap
|
||||
Read in CMAP data for 2 crossterm types
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
Reading data file ...
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10245 atoms
|
||||
reading velocities ...
|
||||
10245 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
15 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
48 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading bonds ...
|
||||
6973 bonds
|
||||
reading angles ...
|
||||
4057 angles
|
||||
reading dihedrals ...
|
||||
1363 dihedrals
|
||||
reading impropers ...
|
||||
70 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
9 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.072 seconds
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
Finding SHAKE clusters ...
|
||||
75 = # of size 2 clusters
|
||||
47 = # of size 3 clusters
|
||||
9 = # of size 4 clusters
|
||||
3265 = # of frozen angles
|
||||
find clusters CPU = 0.003 seconds
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.27938162
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00036407395
|
||||
estimated relative force accuracy = 1.0963718e-06
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 226981 157464
|
||||
Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 2 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmmfsw/coul/long, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 16 1.09 1.38032e-07 6
|
||||
Bond: 18 1.09 1.00046e-07 3
|
||||
Bond: 34 1.111 1.11388e-06 10
|
||||
Bond: 39 1.111 4.83041e-08 5
|
||||
Bond: 43 1.111 1.97842e-07 10
|
||||
Bond: 44 1.111 1.71815e-06 10
|
||||
Bond: 59 1.111 8.42509e-08 2
|
||||
Bond: 62 1.111 2.84854e-08 2
|
||||
Bond: 63 1.111 2.14153e-07 46
|
||||
Bond: 64 1.111 1.59305e-07 18
|
||||
Bond: 65 1.08 5.67061e-07 16
|
||||
Bond: 66 1.08 1.43965e-06 4
|
||||
Bond: 67 1 1.81926e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 1.34571e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 2.71955e-07 6530
|
||||
Bond: 75 1 1.46045e-07 10
|
||||
Bond: 79 0.997 5.24499e-07 17
|
||||
Bond: 81 1 1.32984e-07 4
|
||||
Bond: 84 1.04 7.65389e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 5.75241e-07 2
|
||||
Bond: 97 1.325 4.3613e-08 3
|
||||
Angle: 142 104.52 2.67611e-05 3265
|
||||
Per MPI rank memory allocation (min/avg/max) = 143.6 | 143.6 | 143.6 Mbytes
|
||||
Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
|
||||
0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
|
||||
10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
|
||||
20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
|
||||
30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
|
||||
40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
|
||||
50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
|
||||
60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
|
||||
70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2031
|
||||
80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
|
||||
90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 16 1.09 3.78281e-07 6
|
||||
Bond: 18 1.09 1.12288e-07 3
|
||||
Bond: 34 1.111 7.60709e-07 10
|
||||
Bond: 39 1.111 2.37855e-07 5
|
||||
Bond: 43 1.111 6.00872e-07 10
|
||||
Bond: 44 1.111 3.75324e-07 10
|
||||
Bond: 59 1.111 1.12311e-07 2
|
||||
Bond: 62 1.111 2.99471e-07 2
|
||||
Bond: 63 1.111 6.10589e-07 46
|
||||
Bond: 64 1.111 4.50733e-07 18
|
||||
Bond: 65 1.08 2.90668e-07 16
|
||||
Bond: 66 1.08 1.61592e-07 4
|
||||
Bond: 67 1 5.4508e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 4.1398e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 1.76706e-06 6530
|
||||
Bond: 75 1 3.96686e-07 10
|
||||
Bond: 79 0.997 7.72922e-07 17
|
||||
Bond: 81 1 1.30673e-07 4
|
||||
Bond: 84 1.04 1.44551e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 1.03526e-07 2
|
||||
Bond: 97 1.325 3.64689e-08 3
|
||||
Angle: 142 104.52 0.000130126 3265
|
||||
100 -27913.241 3159.0677 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
|
||||
Loop time of 11.5304 on 1 procs for 100 steps with 10245 atoms
|
||||
|
||||
Performance: 1.499 ns/day, 16.014 hours/ns, 8.673 timesteps/s, 88.852 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 8.6772 | 8.6772 | 8.6772 | 0.0 | 75.25
|
||||
Bond | 0.012444 | 0.012444 | 0.012444 | 0.0 | 0.11
|
||||
Kspace | 1.2286 | 1.2286 | 1.2286 | 0.0 | 10.66
|
||||
Neigh | 1.5276 | 1.5276 | 1.5276 | 0.0 | 13.25
|
||||
Comm | 0.010441 | 0.010441 | 0.010441 | 0.0 | 0.09
|
||||
Output | 0.00055001 | 0.00055001 | 0.00055001 | 0.0 | 0.00
|
||||
Modify | 0.07101 | 0.07101 | 0.07101 | 0.0 | 0.62
|
||||
Other | | 0.002628 | | | 0.02
|
||||
|
||||
Nlocal: 10245 ave 10245 max 10245 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 30479 ave 30479 max 30479 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7.05928e+06 ave 7.05928e+06 max 7.05928e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7059275
|
||||
Ave neighs/atom = 689.04588
|
||||
Ave special neighs/atom = 2.3664226
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:11
|
||||
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.4
Normal file
221
examples/charmmfsw/log.26Jul24.charmmfsw.g++.4
Normal file
@ -0,0 +1,221 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# charmmfsw example generated by https://charmm-gui.org/
|
||||
# from PDB structure 1HVN (https://www.rcsb.org/structure/1HVN)
|
||||
#
|
||||
# Dependencies: packages MOLECULE / KSPACE / RIGID
|
||||
# To test with KOKKOS: lmp -k on g 1 -sf kk -pk kokkos neigh half -in in.charmmfsw
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
|
||||
newton off
|
||||
pair_style lj/charmmfsw/coul/long 10 12
|
||||
Switching to CHARMM coulomb energy conversion constant (src/KSPACE/pair_lj_charmmfsw_coul_long.cpp:63)
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm 1e-6
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmmfsw
|
||||
special_bonds charmm
|
||||
improper_style harmonic
|
||||
timestep 2
|
||||
|
||||
fix cmap all cmap charmmff.cmap
|
||||
Reading CMAP parameters from: charmmff.cmap
|
||||
Read in CMAP data for 2 crossterm types
|
||||
fix_modify cmap energy yes
|
||||
read_data data.charmmfsw.gz fix cmap crossterm CMAP
|
||||
Reading data file ...
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10245 atoms
|
||||
reading velocities ...
|
||||
10245 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
15 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
48 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
orthogonal box = (-24 -24 -24) to (24 24 24)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading bonds ...
|
||||
6973 bonds
|
||||
reading angles ...
|
||||
4057 angles
|
||||
reading dihedrals ...
|
||||
1363 dihedrals
|
||||
reading impropers ...
|
||||
70 impropers
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
4 = max # of 1-2 neighbors
|
||||
9 = max # of 1-3 neighbors
|
||||
17 = max # of 1-4 neighbors
|
||||
21 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.068 seconds
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify delay 2 every 1
|
||||
|
||||
fix 1 all shake 1e-6 100 100 m 1.008 a 142
|
||||
Finding SHAKE clusters ...
|
||||
75 = # of size 2 clusters
|
||||
47 = # of size 3 clusters
|
||||
9 = # of size 4 clusters
|
||||
3265 = # of frozen angles
|
||||
find clusters CPU = 0.001 seconds
|
||||
fix 2 all nvt temp 303.15 303.15 100.0
|
||||
|
||||
thermo 10
|
||||
thermo_style custom step etotal evdwl ecoul elong edihed pe ke temp press
|
||||
|
||||
run 100
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.27938162
|
||||
grid = 54 54 54
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00036407395
|
||||
estimated relative force accuracy = 1.0963718e-06
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 70516 40824
|
||||
Generated 2016 of 2016 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 2 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/charmmfsw/coul/long, perpetual
|
||||
attributes: half, newton off
|
||||
pair build: half/bin/newtoff
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
SHAKE stats (type/ave/delta/count) on step 0
|
||||
Bond: 16 1.09 1.38032e-07 6
|
||||
Bond: 18 1.09 1.00046e-07 3
|
||||
Bond: 34 1.111 1.11388e-06 10
|
||||
Bond: 39 1.111 4.83041e-08 5
|
||||
Bond: 43 1.111 1.97842e-07 10
|
||||
Bond: 44 1.111 1.71815e-06 10
|
||||
Bond: 59 1.111 8.42509e-08 2
|
||||
Bond: 62 1.111 2.84854e-08 2
|
||||
Bond: 63 1.111 2.14153e-07 46
|
||||
Bond: 64 1.111 1.59305e-07 18
|
||||
Bond: 65 1.08 5.67061e-07 16
|
||||
Bond: 66 1.08 1.43965e-06 4
|
||||
Bond: 67 1 1.81926e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 1.34571e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 2.71955e-07 6530
|
||||
Bond: 75 1 1.46045e-07 10
|
||||
Bond: 79 0.997 5.24499e-07 17
|
||||
Bond: 81 1 1.32984e-07 4
|
||||
Bond: 84 1.04 7.65389e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 5.75241e-07 2
|
||||
Bond: 97 1.325 4.3613e-08 3
|
||||
Angle: 142 104.52 2.67611e-05 3265
|
||||
Per MPI rank memory allocation (min/avg/max) = 76.88 | 77.06 | 77.25 Mbytes
|
||||
Step TotEng E_vdwl E_coul E_long E_dihed PotEng KinEng Temp Press
|
||||
0 -27877.652 3447.5013 144035.68 -182420.51 343.05623 -34213.5 6335.8474 307.44113 -989.27065
|
||||
10 -27879.086 3334.4154 144205.4 -182416.19 348.14696 -34133.566 6254.4808 303.49289 -1211.2863
|
||||
20 -27882.193 3293.7931 144272.04 -182415.87 333.20456 -34116.91 6234.7164 302.53384 -1041.5231
|
||||
30 -27886.779 3177.7183 144344.61 -182409.28 340.77044 -34166.241 6279.462 304.70508 -1538.0247
|
||||
40 -27892.698 3186.4294 144409.85 -182417.01 337.80177 -34097.62 6204.9214 301.08807 -1516.1201
|
||||
50 -27898.215 3198.5531 144426.3 -182405.24 336.58074 -34049.909 6151.6947 298.50529 -1349.4431
|
||||
60 -27900.589 3163.4592 144400.32 -182414.85 341.17705 -34110.926 6210.3369 301.35085 -1695.3697
|
||||
70 -27900.487 3223.7183 144242.71 -182409.21 341.09496 -34188.493 6288.0059 305.11967 -1493.2032
|
||||
80 -27901.07 3274.244 144265.07 -182417.68 344.0409 -34177.343 6276.2725 304.55032 -1273.0263
|
||||
90 -27905.672 3237.6056 144288.71 -182418.22 342.15013 -34187.814 6282.1417 304.83511 -1268.0436
|
||||
SHAKE stats (type/ave/delta/count) on step 100
|
||||
Bond: 16 1.09 3.78281e-07 6
|
||||
Bond: 18 1.09 1.12288e-07 3
|
||||
Bond: 34 1.111 7.60709e-07 10
|
||||
Bond: 39 1.111 2.37855e-07 5
|
||||
Bond: 43 1.111 6.00872e-07 10
|
||||
Bond: 44 1.111 3.75324e-07 10
|
||||
Bond: 59 1.111 1.12311e-07 2
|
||||
Bond: 62 1.111 2.99471e-07 2
|
||||
Bond: 63 1.111 6.10589e-07 46
|
||||
Bond: 64 1.111 4.50733e-07 18
|
||||
Bond: 65 1.08 2.90668e-07 16
|
||||
Bond: 66 1.08 1.61592e-07 4
|
||||
Bond: 67 1 5.4508e-07 10
|
||||
Bond: 68 1.01 0 1
|
||||
Bond: 69 1.08 4.1398e-07 5
|
||||
Bond: 70 1.09 0 1
|
||||
Bond: 71 1.083 0 1
|
||||
Bond: 72 0.9572 1.76706e-06 6530
|
||||
Bond: 75 1 3.96686e-07 10
|
||||
Bond: 79 0.997 7.72922e-07 17
|
||||
Bond: 81 1 1.30673e-07 4
|
||||
Bond: 84 1.04 1.44551e-07 9
|
||||
Bond: 87 1 0 1
|
||||
Bond: 95 0.96 1.03526e-07 2
|
||||
Bond: 97 1.325 3.64689e-08 3
|
||||
Angle: 142 104.52 0.000130126 3265
|
||||
100 -27913.241 3159.0676 144299.1 -182414.94 336.48839 -34254.412 6341.1706 307.69943 -1421.2905
|
||||
Loop time of 3.49837 on 4 procs for 100 steps with 10245 atoms
|
||||
|
||||
Performance: 4.939 ns/day, 4.859 hours/ns, 28.585 timesteps/s, 292.851 katom-step/s
|
||||
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.4572 | 2.5133 | 2.5634 | 2.6 | 71.84
|
||||
Bond | 0.0040264 | 0.0050718 | 0.0069286 | 1.6 | 0.14
|
||||
Kspace | 0.45979 | 0.50903 | 0.56364 | 5.6 | 14.55
|
||||
Neigh | 0.42029 | 0.42034 | 0.42036 | 0.0 | 12.02
|
||||
Comm | 0.013207 | 0.013292 | 0.013404 | 0.1 | 0.38
|
||||
Output | 0.00026525 | 0.00029549 | 0.00038249 | 0.0 | 0.01
|
||||
Modify | 0.035024 | 0.035546 | 0.03621 | 0.3 | 1.02
|
||||
Other | | 0.001504 | | | 0.04
|
||||
|
||||
Nlocal: 2561.25 ave 2599 max 2520 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 16491.5 ave 16541 max 16442 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 1.99855e+06 ave 2.04035e+06 max 1.95468e+06 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 7994217
|
||||
Ave neighs/atom = 780.30425
|
||||
Ave special neighs/atom = 2.3664226
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:03
|
||||
Reference in New Issue
Block a user