345 lines
13 KiB
Groff
345 lines
13 KiB
Groff
LAMMPS (27 Jun 2024)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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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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Reading data file ...
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orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
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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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orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
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1 by 1 by 1 MPI processor grid
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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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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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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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special bonds CPU = 0.000 seconds
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read_data CPU = 0.012 seconds
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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 peptide2.colvars.*"
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fix 2 all colvars peptide.colvars2 output peptide2
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----------------------------------------------------------------------
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Initializing the collective variables module, version 2024-06-04.
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Please cite Fiorin et al, Mol Phys 2013:
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https://doi.org/10.1080/00268976.2013.813594
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as well as all other papers listed below for individual features used.
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Please cite Fiorin et al, Mol Phys 2013:
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https://doi.org/10.1080/00268976.2013.813594
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as well as all other papers listed below for individual features used.
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Please cite Fiorin et al, Mol Phys 2013:
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https://doi.org/10.1080/00268976.2013.813594
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as well as all other papers listed below for individual features used.
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This version was built with the C++11 standard or higher.
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Summary of compile-time features available in this build:
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- SMP parallelism: enabled (num. threads = 1)
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- Lepton custom functions: available
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- Tcl interpreter: not available
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Using LAMMPS interface, version "2024-07-05".
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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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Finding SHAKE clusters ...
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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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find clusters CPU = 0.000 seconds
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#dump 1 colvar custom 1 dump.colvar2.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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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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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},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282–-3297}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.26872465
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.022820853
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estimated relative force accuracy = 6.872432e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 10648 3375
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Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
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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
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bin: standard
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----------------------------------------------------------------------
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Reading new configuration from file "peptide.colvars2":
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# units = "" [default]
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# smp = on [default]
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# colvarsTrajFrequency = 1
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# colvarsRestartFrequency = 1000
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# scriptedColvarForces = off [default]
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# scriptingAfterBiases = off [default]
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----------------------------------------------------------------------
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Initializing a new collective variable.
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# name = "one"
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Initializing a new "distance" component.
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# name = "" [default]
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# componentCoeff = 1 [default]
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# componentExp = 1 [default]
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# period = 0 [default]
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# wrapAround = 0 [default]
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# forceNoPBC = off [default]
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# scalable = on [default]
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Initializing atom group "group1".
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# name = "" [default]
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# centerToOrigin = off [default]
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# centerToReference = off [default]
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# rotateToReference = off [default]
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# atomsOfGroup = "" [default]
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# indexGroup = "" [default]
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# psfSegID = [default]
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# atomsFile = "" [default]
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# dummyAtom = ( 0 , 0 , 0 ) [default]
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# enableFitGradients = on [default]
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# printAtomIDs = off [default]
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Atom group "group1" defined with 4 atoms requested.
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Initializing atom group "group2".
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# name = "" [default]
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# centerToOrigin = off [default]
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# centerToReference = off [default]
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# rotateToReference = off [default]
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# atomsOfGroup = "" [default]
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# indexGroup = "" [default]
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# psfSegID = [default]
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# atomsFile = "" [default]
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# dummyAtom = ( 0 , 0 , 0 ) [default]
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# enableFitGradients = on [default]
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# printAtomIDs = off [default]
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Atom group "group2" defined with 4 atoms requested.
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# oneSiteSystemForce = off [default]
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# oneSiteTotalForce = off [default]
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All components initialized.
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# timeStepFactor = 1 [default]
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# width = 1 [default]
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# lowerBoundary = 0 [default]
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# upperBoundary = 1 [default]
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# hardLowerBoundary = on [default]
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# hardUpperBoundary = off [default]
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# expandBoundaries = off [default]
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# extendedLagrangian = off [default]
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# outputValue = on [default]
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# outputVelocity = off [default]
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# outputTotalForce = off [default]
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# outputAppliedForce = off [default]
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# subtractAppliedForce = off [default]
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# runAve = off [default]
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# corrFunc = off [default]
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----------------------------------------------------------------------
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Collective variables initialized, 1 in total.
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----------------------------------------------------------------------
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Initializing a new "harmonic" instance.
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# name = "h_pot"
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# colvars = { one }
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# stepZeroData = off [default]
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# outputEnergy = off [default]
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# outputFreq = 1000 [default]
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# timeStepFactor = 1 [default]
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# writeTISamples = off [default]
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# writeTIPMF = off [default]
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# centers = { 10 }
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# targetCenters = { 10 } [default]
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# outputCenters = off [default]
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# forceConstant = 100
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# decoupling = off [default]
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# targetForceConstant = -1 [default]
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The force constant for colvar "one" will be rescaled to 100 according to the specified width (1).
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----------------------------------------------------------------------
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Collective variables biases initialized, 1 in total.
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----------------------------------------------------------------------
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Collective variables module (re)initialized.
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----------------------------------------------------------------------
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Current simulation parameters: initial step = 0, integration timestep = 2
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Updating atomic parameters (masses, charges, etc).
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Re-initialized atom group for variable "one":0/0. 4 atoms: total mass = 15.035, total charge = -2.77556e-17.
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Re-initialized atom group for variable "one":0/1. 4 atoms: total mass = 15.035, total charge = 0.16.
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The final output state file will be "peptide2.colvars.state".
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Synchronizing (emptying the buffer of) trajectory file "peptide2.colvars.traj".
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SHAKE stats (type/ave/delta/count) on step 0
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Bond: 4 1.111 1.44264e-05 9
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Bond: 6 0.996998 7.26967e-06 6
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Bond: 8 1.08 1.32536e-05 7
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Bond: 10 1.111 1.22749e-05 8
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Bond: 12 1.08 1.11767e-05 9
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Bond: 14 0.96 0 1
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Bond: 18 0.957206 4.37979e-05 1280
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Angle: 31 104.519 0.00396029 640
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Per MPI rank memory allocation (min/avg/max) = 19.03 | 19.03 | 19.03 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 273.74323
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10 333.47919 -4982.3968 -6324.0169 1341.6201 -6400.4223 21.367762 12.393263
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20 309.56902 -4999.4978 -6244.9249 1245.4271 -6401.6981 43.59542 13.004314
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30 316.9763 -5025.5662 -6300.7935 1275.2273 -6422.5375 27.323196 6.7589585
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40 297.55779 -5088.2204 -6285.3252 1197.1047 -6395.375 13.6769 25.625024
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50 296.79994 -5117.2966 -6311.3525 1194.0558 -6451.8309 30.631241 5.3320863
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60 281.72778 -5188.4969 -6321.9159 1133.419 -6427.8856 26.287723 20.574037
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70 277.26053 -5224.8434 -6340.2902 1115.4468 -6447.8521 27.742893 0.69420283
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80 268.01484 -5281.8509 -6360.1014 1078.2505 -6496.6086 20.300754 5.2607186
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90 270.43472 -5334.0835 -6422.0694 1087.9859 -6563.2511 39.846095 1.1832272
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SHAKE stats (type/ave/delta/count) on step 100
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Bond: 4 1.11096 0.000191462 9
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Bond: 6 0.996989 3.55508e-05 6
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Bond: 8 1.08 9.0997e-06 7
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Bond: 10 1.111 1.58544e-05 8
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Bond: 12 1.08 5.80604e-06 9
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Bond: 14 0.959997 0 1
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Bond: 18 0.957198 2.92445e-05 1280
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Angle: 31 104.52 0.00239923 640
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100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
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Saving collective variables state to "peptide2.colvars.state".
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Loop time of 0.907882 on 1 procs for 100 steps with 2004 atoms
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Performance: 19.033 ns/day, 1.261 hours/ns, 110.146 timesteps/s, 220.734 katom-step/s
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99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.71563 | 0.71563 | 0.71563 | 0.0 | 78.82
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Bond | 0.0013267 | 0.0013267 | 0.0013267 | 0.0 | 0.15
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Kspace | 0.042157 | 0.042157 | 0.042157 | 0.0 | 4.64
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Neigh | 0.13452 | 0.13452 | 0.13452 | 0.0 | 14.82
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Comm | 0.0034995 | 0.0034995 | 0.0034995 | 0.0 | 0.39
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Output | 0.00014584 | 0.00014584 | 0.00014584 | 0.0 | 0.02
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Modify | 0.010115 | 0.010115 | 0.010115 | 0.0 | 1.11
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Other | | 0.0004888 | | | 0.05
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Nlocal: 2004 ave 2004 max 2004 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11143 ave 11143 max 11143 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 708234 ave 708234 max 708234 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 708234
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Ave neighs/atom = 353.41018
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Ave special neighs/atom = 2.3403194
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Neighbor list builds = 13
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Dangerous builds = 1
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- Colvars module (Fiorin2013, plus other works listed for specific features)
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% Colvars module:
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% Colvars-LAMMPS interface:
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% Harmonic colvar bias implementation:
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% Optimal rotation via flexible fitting:
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% distance colvar component:
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@article{Fiorin2013,
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author = {Fiorin, Giacomo and Klein, Michael L.{} and H\'enin, J\'er\^ome},
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title = {Using collective variables to drive molecular dynamics simulations},
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journal = {Mol. Phys.},
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year = {2013},
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volume = {111},
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number = {22-23},
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pages = {3345--3362},
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publisher = {Taylor & Francis},
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doi = {10.1080/00268976.2013.813594},
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url = {https://doi.org/10.1080/00268976.2013.813594}
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}
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% LAMMPS engine:
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@article{Thompson2022,
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title = {{LAMMPS} - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales},
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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.},
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journal = {Comp. Phys. Comm.},
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volume = {271},
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pages = {108171},
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year = {2022},
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doi = {10.1016/j.cpc.2021.108171},
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url = {https://doi.org/10.1016/j.cpc.2021.108171}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Total wall time: 0:00:00
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