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 1 by 1 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 = 10648 3375 5808
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 = 22.5866 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 35.344163 10.563914
40 297.87524 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.723201 3.8354392
50 304.02086 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459508 0.20679801
60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.76729 0.69356508
70 277.835 -5163.9752 -6281.7332 1117.758 -6447.7015 39.627148 11.433632
80 267.51473 -5206.4042 -6282.6427 1076.2385 -6456.6352 31.611843 6.3553235
90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8037 28.849899 0.36938867
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
100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 2.39102 on 1 procs for 100 steps with 2004 atoms
Pair time (%) = 1.86583 (78.0347)
Bond time (%) = 0.00628591 (0.262896)
Kspace time (%) = 0.165128 (6.90614)
Neigh time (%) = 0.314792 (13.1656)
Comm time (%) = 0.0111108 (0.464687)
Output time (%) = 0.000252724 (0.0105697)
Modify time (%) = 0.0253747 (1.06125)
Other time (%) = 0.0022521 (0.0941899)
FFT time (% of Kspce) = 0.0274372 (16.6158)
FFT Gflps 3d (1d only) = 1.99867 2.86506
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 ...
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 = 10648 3375 5808
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 = 3900175693153042431
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 = 22.5866 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
110 266.26278 -5341.2103 -6412.412 1071.2018 -6552.7583 33.572968 1.9229782
120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859553 2.7124877
130 252.8344 -5422.5446 -6439.7226 1017.1781 -6580.4752 25.979049 1.2031628
140 253.85115 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071514 0.30586247
150 261.31825 -5490.48 -6541.7895 1051.3095 -6646.6144 16.258548 6.9049974
160 255.7368 -5521.6048 -6550.4596 1028.8547 -6658.1517 19.717533 12.339821
170 253.42877 -5540.1003 -6559.6695 1019.5693 -6656.6878 23.293662 10.289878
180 248.51086 -5550.3244 -6550.1084 999.78404 -6661.4182 26.200056 3.4339065
190 250.8039 -5555.2614 -6564.2706 1009.0092 -6666.15 25.536594 3.3495152
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.8129e-06
6 0.997 7.7964e-07
8 1.08 1.08934e-06
10 1.111 2.96501e-07
12 1.08 4.69174e-07
14 0.960001 0
18 0.957201 3.76571e-06
31 104.52 0.000411068
200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 2.23495 on 1 procs for 100 steps with 2004 atoms
Pair time (%) = 1.84544 (82.572)
Bond time (%) = 0.00609159 (0.27256)
Kspace time (%) = 0.163201 (7.30223)
Neigh time (%) = 0.183405 (8.20622)
Comm time (%) = 0.00959301 (0.429227)
Output time (%) = 0.000245094 (0.0109664)
Modify time (%) = 0.0247326 (1.10663)
Other time (%) = 0.00223875 (0.10017)
FFT time (% of Kspce) = 0.0272989 (16.7271)
FFT Gflps 3d (1d only) = 2.0088 2.93901
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: 708088 ave 708088 max 708088 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708088
Ave neighs/atom = 353.337
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 = 10648 3375 5808
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 = 3900175693153042431
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 7.7964e-07
8 1.08 1.08934e-06
10 1.111 2.96501e-07
12 1.08 4.69174e-07
14 0.960001 0
18 0.957201 3.76571e-06
31 104.52 0.000411068
Memory usage per processor = 22.5866 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
210 253.15043 -5538.5668 -6557.0163 1018.4495 -6672.041 37.67158 0.61296982
220 245.19746 -5522.5242 -6508.9781 986.4539 -6628.1999 36.656356 0.048624555
230 258.65299 -5495.7177 -6536.3046 1040.5868 -6658.0952 34.855726 0.22046598
240 260.80143 -5469.8517 -6519.0819 1049.2302 -6624.1723 31.576409 3.7570726
250 269.06507 -5438.3971 -6520.8727 1082.4757 -6616.3871 25.444125 8.6640978
260 266.10282 -5397.3162 -6467.8744 1070.5583 -6580.628 26.873936 8.3330854
270 272.81993 -5350.8393 -6448.4211 1097.5819 -6563.8139 23.113421 10.972906
280 279.52079 -5307.9855 -6432.5256 1124.5401 -6557.7274 33.641095 8.5474821
290 286.81184 -5260.8728 -6414.7455 1153.8727 -6515.5418 28.572468 5.9092648
SHAKE stats (type/ave/delta) on step 300
4 1.111 1.79733e-05
6 0.997005 1.02622e-05
8 1.08 1.84996e-05
10 1.111 9.98595e-06
12 1.08 8.83195e-06
14 0.960008 0
18 0.957203 1.84801e-05
31 104.52 0.00169221
300 291.51842 -5216.3285 -6389.1362 1172.8077 -6503.1141 27.877464 2.2482411
colvars: Saving collective variables state to "out2.colvars.state".
Loop time of 2.25031 on 1 procs for 100 steps with 2004 atoms
Pair time (%) = 1.83745 (81.6533)
Bond time (%) = 0.00609803 (0.270987)
Kspace time (%) = 0.162178 (7.20694)
Neigh time (%) = 0.207886 (9.23812)
Comm time (%) = 0.00977254 (0.434276)
Output time (%) = 0.000240803 (0.0107009)
Modify time (%) = 0.024461 (1.08701)
Other time (%) = 0.00221944 (0.0986283)
FFT time (% of Kspce) = 0.0273609 (16.8709)
FFT Gflps 3d (1d only) = 2.00425 2.94806
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11292 ave 11292 max 11292 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708145 ave 708145 max 708145 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708145
Ave neighs/atom = 353.366
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0