261 lines
10 KiB
Groff
261 lines
10 KiB
Groff
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 peptide2.colvars.*"
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fix 2 all colvars peptide.colvars2 output peptide2
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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.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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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.colvars2":
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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, 4 atoms initialized: total mass = 4, 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, 1 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 }
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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 }
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colvars: # targetCenters = { 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. 4 atoms: total mass = 4.
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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 "peptide2.colvars.state".
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colvars: Writing to colvar trajectory file "peptide2.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. 4 atoms: total mass = 15.035.
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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 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) on step 100
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4 1.11096 0.000191462
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6 0.996989 3.55508e-05
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8 1.08 9.0997e-06
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10 1.111 1.58544e-05
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12 1.08 5.80604e-06
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14 0.959997 0
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18 0.957198 2.92445e-05
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31 104.52 0.00239923
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100 260.35636 -5387.2284 -6434.6681 1047.4397 -6534.1956 20.246866 0.075048487
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colvars: Saving collective variables state to "peptide2.colvars.state".
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Loop time of 2.25958 on 1 procs for 100 steps with 2004 atoms
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Performance: 7.647 ns/day, 3.138 hours/ns, 44.256 timesteps/s
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99.8% 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 | 1.6373 | 1.6373 | 1.6373 | 0.0 | 72.46
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Bond | 0.0031531 | 0.0031531 | 0.0031531 | 0.0 | 0.14
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Kspace | 0.17439 | 0.17439 | 0.17439 | 0.0 | 7.72
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Neigh | 0.40442 | 0.40442 | 0.40442 | 0.0 | 17.90
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Comm | 0.014091 | 0.014091 | 0.014091 | 0.0 | 0.62
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Output | 0.00027752 | 0.00027752 | 0.00027752 | 0.0 | 0.01
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Modify | 0.024481 | 0.024481 | 0.024481 | 0.0 | 1.08
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Other | | 0.001465 | | | 0.06
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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 = 353.41
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 13
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Dangerous builds = 1
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colvars: Resetting the Collective Variables module.
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:02
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