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lammps/examples/USER/colvars/log.peptide.colvars
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LAMMPS (5 Mar 2012-ICMS)
# 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
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
2 by 2 by 2 MPI processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
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 ...
G vector (1/distance) = 0.268721
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.01614
estimated relative force accuracy = 4.86052e-05
using single precision FFTs
brick FFT buffer size/proc = 2744 512 2352
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-03.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out.colvars.state".
colvars: The trajectory file will be "out.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = one
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = two
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0 [default]
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 0 [default]
colvars: # upperWallConstant = 0 [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = off [default]
colvars: # outputAppliedForce = 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: # forceConstant = 100
colvars: # centers = { 10, 10 }
colvars: # targetCenters = { 10, 10 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
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
Memory usage per processor = 9.38579 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604
10 305.06198 -5058.8899 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
20 311.00592 -4999.0544 -6250.2623 1251.2079 -6417.0984 47.695274 36.699706
30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344162 10.563914
40 297.87524 -5020.8338 -6219.2157 1198.3819 -6389.85 27.723201 3.8354392
50 304.02086 -5056.254 -6279.3603 1223.1063 -6456.8182 55.459508 0.20679799
60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.767289 0.69356505
70 277.835 -5163.9752 -6281.7332 1117.758 -6447.7014 39.627148 11.433632
80 267.51474 -5206.4042 -6282.6428 1076.2385 -6456.6352 31.611843 6.3553237
90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8037 28.849899 0.36938877
SHAKE stats (type/ave/delta) on step 100
4 1.11098 8.97184e-05
6 0.996996 1.00568e-05
8 1.08 6.02345e-06
10 1.111 1.84257e-05
12 1.08 7.27136e-06
14 0.959996 0
18 0.957198 3.36077e-05
31 104.52 0.00306008
100 260.10504 -5292.6891 -6339.1177 1046.4286 -6471.6693 25.361886 0.21986867
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 0.443301 on 8 procs for 100 steps with 2004 atoms
Pair time (%) = 0.245459 (55.3708)
Bond time (%) = 0.00108373 (0.244468)
Kspace time (%) = 0.0620093 (13.9881)
Neigh time (%) = 0.0400429 (9.03288)
Comm time (%) = 0.0573151 (12.9292)
Output time (%) = 0.0120609 (2.7207)
Modify time (%) = 0.0223317 (5.03759)
Other time (%) = 0.0029982 (0.676335)
FFT time (% of Kspce) = 0.00953376 (15.3747)
FFT Gflps 3d (1d only) = 5.75198 19.7389
Nlocal: 250.5 ave 263 max 235 min
Histogram: 1 0 1 1 0 1 2 0 0 2
Nghost: 4925.75 ave 4965 max 4880 min
Histogram: 1 0 1 0 3 0 0 1 0 2
Neighs: 88529.6 ave 93144 max 82125 min
Histogram: 1 0 0 2 0 1 1 1 0 2
Total # of neighbors = 708237
Ave neighs/atom = 353.412
Ave special neighs/atom = 2.34032
Neighbor list builds = 12
Dangerous builds = 2
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