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lammps/examples/USER/colvars/log.peptide-colvars-4
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LAMMPS (21 May 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)
1 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 = 4312 960 3696
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
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 = 10.1924 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 -5058.8898 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
20 311.00592 -4999.0545 -6250.2624 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 -5020.8339 -6219.2157 1198.3819 -6389.85 27.723201 3.8354392
50 304.02086 -5056.254 -6279.3603 1223.1063 -6456.8182 55.459508 0.206798
60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.767289 0.69356507
70 277.835 -5163.9751 -6281.7331 1117.758 -6447.7014 39.627147 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 -6499.8036 28.849898 0.36938879
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 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 0.686681 on 4 procs for 100 steps with 2004 atoms
Pair time (%) = 0.47104 (68.5966)
Bond time (%) = 0.00184608 (0.26884)
Kspace time (%) = 0.0808357 (11.7719)
Neigh time (%) = 0.0772016 (11.2427)
Comm time (%) = 0.0293136 (4.26888)
Output time (%) = 0.000323951 (0.0471764)
Modify time (%) = 0.0247293 (3.60128)
Other time (%) = 0.00139064 (0.202516)
FFT time (% of Kspce) = 0.0117171 (14.4949)
FFT Gflps 3d (1d only) = 4.68018 10.009
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 181741 max 172943 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 ...
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 = 4312 960 3696
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
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: Restarting from file "out.colvars.state".
colvars: Restarting collective variable "one" from value: 10.0137
colvars: Restarting collective variable "two" from value: 10.0649
colvars: Restarting harmonic bias "h_pot".
colvars: Reading current stage from the restart.
colvars: # stage = 8103505641670189088
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
colvars: Initializing step number as firstTimestep.
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
Memory usage per processor = 10.1967 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
100 260.10504 -5292.6891 -6339.1176 1046.4286 -6471.6693 25.361886 0.21986866
110 266.26278 -5341.2101 -6412.4119 1071.2018 -6552.7582 33.572969 1.9229778
120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859555 2.7124877
130 252.83442 -5422.5444 -6439.7226 1017.1781 -6580.4752 25.979048 1.2031628
140 253.85116 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071518 0.30586252
150 261.31828 -5490.48 -6541.7895 1051.3096 -6646.6145 16.25855 6.9049978
160 255.73681 -5521.6048 -6550.4596 1028.8548 -6658.1518 19.717536 12.339819
170 253.42879 -5540.1004 -6559.6697 1019.5694 -6656.688 23.293657 10.289879
180 248.51083 -5550.3244 -6550.1084 999.78393 -6661.4181 26.200057 3.433906
190 250.80387 -5555.2613 -6564.2703 1009.009 -6666.1497 25.536596 3.3495164
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.8129e-06
6 0.997 7.79639e-07
8 1.08 1.08934e-06
10 1.111 2.96501e-07
12 1.08 4.69175e-07
14 0.960001 0
18 0.957201 3.76571e-06
31 104.52 0.000411069
200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 0.653275 on 4 procs for 100 steps with 2004 atoms
Pair time (%) = 0.47279 (72.3723)
Bond time (%) = 0.00182116 (0.278774)
Kspace time (%) = 0.079544 (12.1762)
Neigh time (%) = 0.0451868 (6.91696)
Comm time (%) = 0.027427 (4.19838)
Output time (%) = 0.000316501 (0.0484483)
Modify time (%) = 0.0247022 (3.78129)
Other time (%) = 0.00148731 (0.227671)
FFT time (% of Kspce) = 0.0109947 (13.8221)
FFT Gflps 3d (1d only) = 4.98769 10.1728
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: 177022 ave 182261 max 172093 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 708086
Ave neighs/atom = 353.336
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
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 = 4312 960 3696
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-23.
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 "out2.colvars.state".
colvars: The trajectory file will be "out2.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: 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: Restarting harmonic bias "h_pot".
colvars: Reading current stage from the restart.
colvars: # stage = 8103505641670189088
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
colvars: Initializing step number as firstTimestep.
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.8129e-06
6 0.997 7.79639e-07
8 1.08 1.08934e-06
10 1.111 2.96501e-07
12 1.08 4.69175e-07
14 0.960001 0
18 0.957201 3.76571e-06
31 104.52 0.000411069
Memory usage per processor = 10.201 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
200 251.50575 -5557.4209 -6569.2537 1011.8328 -6674.0864 24.805164 7.1388874
210 253.15047 -5538.5669 -6557.0165 1018.4497 -6672.0412 37.671574 0.61297094
220 245.19752 -5522.5242 -6508.9784 986.45412 -6628.2001 36.656348 0.048624447
230 258.65297 -5495.7177 -6536.3044 1040.5868 -6658.0951 34.855726 0.22046446
240 260.8016 -5469.8518 -6519.0827 1049.2309 -6624.173 31.576408 3.757081
250 269.06524 -5438.3971 -6520.8735 1082.4764 -6616.3878 25.444134 8.6641098
260 266.10241 -5397.317 -6467.8736 1070.5566 -6580.6272 26.87393 8.333095
270 272.82004 -5350.8402 -6448.4225 1097.5823 -6563.8152 23.113398 10.972914
280 279.52006 -5307.9867 -6432.5238 1124.5371 -6557.7256 33.641067 8.5474809
290 286.81221 -5260.8707 -6414.7449 1153.8742 -6515.5413 28.572449 5.9092582
SHAKE stats (type/ave/delta) on step 300
4 1.111 1.79733e-05
6 0.997005 1.02621e-05
8 1.08 1.84996e-05
10 1.111 9.98591e-06
12 1.08 8.83192e-06
14 0.960008 0
18 0.957203 1.84805e-05
31 104.52 0.00169223
300 291.51901 -5216.3298 -6389.1399 1172.8101 -6503.1178 27.877408 2.2482392
colvars: Saving collective variables state to "out2.colvars.state".
Loop time of 0.662081 on 4 procs for 100 steps with 2004 atoms
Pair time (%) = 0.47307 (71.452)
Bond time (%) = 0.00178617 (0.269781)
Kspace time (%) = 0.0802494 (12.1208)
Neigh time (%) = 0.0528576 (7.98355)
Comm time (%) = 0.0277618 (4.19311)
Output time (%) = 0.000293612 (0.0443469)
Modify time (%) = 0.0245907 (3.71416)
Other time (%) = 0.00147164 (0.222275)
FFT time (% of Kspce) = 0.011487 (14.3141)
FFT Gflps 3d (1d only) = 4.77392 9.91625
Nlocal: 501 ave 514 max 471 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Nghost: 6609.75 ave 6681 max 6555 min
Histogram: 1 1 0 0 0 1 0 0 0 1
Neighs: 177036 ave 180240 max 169752 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Total # of neighbors = 708146
Ave neighs/atom = 353.366
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
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