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LAMMPS (28 Oct 2014-ICMS)
WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:88)
using 1 OpenMP thread(s) per MPI task
# 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
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 2 MPI processor grid
reading atoms ...
2004 atoms
reading velocities ...
2004 velocities
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
14 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
1365 bonds
reading angles ...
786 angles
reading dihedrals ...
207 dihedrals
reading impropers ...
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.* out*.abf.* out*.meta.*"
fix 2 all colvars peptide.meta tstat 1
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) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2014-10-29.
colvars: Using LAMMPS interface, version 2014-10-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.meta":
colvars: # indexFile = "" [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # colvarsTrajAppend = off [default]
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: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 20
colvars: # upperWallConstant = 0 [default]
colvars: # hardLowerBoundary = on
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = on
colvars: # outputAppliedForce = on
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: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 20
colvars: # upperWallConstant = 0 [default]
colvars: # hardLowerBoundary = on
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = on
colvars: # outputAppliedForce = on
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = abf
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # applyBias = off
colvars: WARNING: ABF biases will *not* be applied!
colvars: # updateBias = on [default]
colvars: # hideJacobian = off [default]
colvars: Jacobian (geometric) forces will be included in reported free energy gradients.
colvars: # fullSamples = 200 [default]
colvars: # inputPrefix = [default]
colvars: # outputFreq = 1000 [default]
colvars: # historyFreq = 0 [default]
colvars: # shared = off [default]
colvars: # maxForce = [default]
colvars: Finished ABF setup.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "histogram" instance.
colvars: # name = histo
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # outputfreq = 1000 [default]
colvars: Finished histogram setup.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "metadynamics" instance.
colvars: # name = meta
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: Warning: running ABF and metadynamics together is not recommended unless applyBias is off for ABF.
colvars: # hillWeight = 0.01
colvars: # newHillFrequency = 1000 [default]
colvars: # hillWidth = 1.25331 [default]
colvars: # multipleReplicas = off [default]
colvars: # useGrids = on [default]
colvars: # gridsUpdateFrequency = 1000 [default]
colvars: # rebinGrids = off [default]
colvars: # keepHills = off [default]
colvars: # writeFreeEnergyFile = on [default]
colvars: # saveFreeEnergyFile = off [default]
colvars: # writeHillsTrajectory = off [default]
colvars: # wellTempered = off [default]
colvars: # biasTemperature = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 3 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out.colvars.state".
colvars: Writing to colvar trajectory file "out.colvars.traj".
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Prepared sample and gradient buffers at step 0.
colvars: Histogram histo will be written to file "out.histo.dat"
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 = 14.8029 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0.0077900402
10 277.56212 -5234.5263 -6351.1864 1116.6601 -6421.6671 15.157588 0.0066001406
20 279.23937 -5226.3701 -6349.778 1123.4079 -6438.8931 20.18301 0.0066001406
30 282.18549 -5222.2084 -6357.4688 1135.2604 -6447.4794 20.633957 0.0066001406
40 275.79443 -5220.6006 -6330.1492 1109.5485 -6418.1923 12.957978 0.0066001406
50 285.29494 -5218.0673 -6365.8373 1147.7701 -6444.2366 16.492937 0.0066001406
60 271.8089 -5220.1134 -6313.6278 1093.5144 -6406.0206 20.0835 0.0066001406
70 273.78869 -5224.3651 -6325.8443 1101.4793 -6411.4896 20.115756 0.0066001406
80 273.59851 -5228.1216 -6328.8358 1100.7142 -6417.5964 17.279319 0.0066001406
90 285.15981 -5229.7427 -6376.9691 1147.2264 -6462.8913 25.416892 0.0066001406
SHAKE stats (type/ave/delta) on step 100
4 1.111 1.94821e-06
6 0.996999 1.95443e-06
8 1.08 1.31368e-06
10 1.111 1.50165e-06
12 1.08 7.11595e-07
14 0.959999 0
18 0.9572 9.09647e-06
31 104.52 0.000738854
100 271.72192 -5234.6681 -6327.8325 1093.1645 -6417.4352 16.437782 0.0022862156
Loop time of 1.05115 on 2 procs for 100 steps with 2004 atoms
98.8% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.439 ns/day 1.460 hours/ns 95.134 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.8083 | 0.81185 | 0.81541 | 0.4 | 77.23
Bond | 0.002435 | 0.0026462 | 0.0028574 | 0.4 | 0.25
Kspace | 0.092542 | 0.095508 | 0.098474 | 1.0 | 9.09
Neigh | 0.092974 | 0.092999 | 0.093023 | 0.0 | 8.85
Comm | 0.016783 | 0.017117 | 0.017452 | 0.3 | 1.63
Output | 0.00023127 | 0.00032663 | 0.000422 | 0.5 | 0.03
Modify | 0.028247 | 0.028249 | 0.02825 | 0.0 | 2.69
Other | | 0.002451 | | | 0.23
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8643.5 ave 8659 max 8628 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354020 ave 356051 max 351989 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708040
Ave neighs/atom = 353.313
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
run 100
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
SHAKE stats (type/ave/delta) on step 100
4 1.111 1.94821e-06
6 0.996999 1.95443e-06
8 1.08 1.31368e-06
10 1.111 1.50165e-06
12 1.08 7.11595e-07
14 0.959999 0
18 0.9572 9.09647e-06
31 104.52 0.000738854
Memory usage per processor = 14.8029 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
100 271.72192 -5234.6681 -6327.8325 1093.1645 -6417.4352 16.437782 0.0022862156
110 282.16031 -5238.8517 -6374.0108 1135.1591 -6468.9774 26.412073 0.0022862156
120 279.45426 -5243.5439 -6367.8163 1124.2724 -6463.8685 26.028966 0.0022862156
130 271.89688 -5252.2256 -6346.094 1093.8683 -6438.0184 17.495971 0.00015177801
140 272.07608 -5263.1471 -6357.7363 1094.5893 -6448.0579 24.579379 0.0022862156
150 273.22606 -5275.1371 -6374.3528 1099.2157 -6457.5278 20.618959 0.0022862156
160 283.3293 -5284.065 -6423.9271 1139.8621 -6508.5083 17.883412 0.0022862156
170 276.88372 -5293.031 -6406.9619 1113.9309 -6497.0534 18.814415 0.0022862156
180 276.528 -5304.7997 -6417.2995 1112.4998 -6498.7751 18.00968 0.0022862156
190 274.63131 -5315.0102 -6419.8794 1104.8692 -6500.8893 13.339942 0.0022862156
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.87411e-06
6 0.996999 3.05638e-06
8 1.08 1.82265e-06
10 1.111 1.92009e-06
12 1.08 1.96521e-06
14 0.959999 0
18 0.9572 1.13163e-05
31 104.52 0.00114656
200 280.25149 -5323.7989 -6451.2787 1127.4798 -6532.4552 19.301584 0.0022862156
Loop time of 1.05726 on 2 procs for 100 steps with 2004 atoms
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.344 ns/day 1.468 hours/ns 94.584 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.81472 | 0.81648 | 0.81824 | 0.2 | 77.23
Bond | 0.0025082 | 0.002708 | 0.0029078 | 0.4 | 0.26
Kspace | 0.094113 | 0.095593 | 0.097073 | 0.5 | 9.04
Neigh | 0.093044 | 0.093048 | 0.093053 | 0.0 | 8.80
Comm | 0.017248 | 0.017325 | 0.017401 | 0.1 | 1.64
Output | 0.00023341 | 0.00033283 | 0.00043225 | 0.5 | 0.03
Modify | 0.029212 | 0.029252 | 0.029293 | 0.0 | 2.77
Other | | 0.002524 | | | 0.24
Nlocal: 1002 ave 1003 max 1001 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8631 ave 8646 max 8616 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 353970 ave 356541 max 351400 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 707941
Ave neighs/atom = 353.264
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
fix 2 all colvars peptide.meta input out.colvars.state tstat 1 output out2
colvars: Saving collective variables state to "out.colvars.state".
colvars: Resetting the Collective Variables Module.
run 100
PPPM initialization ...
G vector (1/distance) = 0.268725
grid = 15 15 15
stencil order = 5
estimated absolute RMS force accuracy = 0.0228209
estimated relative force accuracy = 6.87243e-05
using double precision FFTs
3d grid and FFT values/proc = 6776 1800
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2014-10-29.
colvars: Using LAMMPS interface, version 2014-10-29.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.meta":
colvars: # indexFile = "" [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 1
colvars: # colvarsRestartFrequency = 1000
colvars: # colvarsTrajAppend = off [default]
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: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 20
colvars: # upperWallConstant = 0 [default]
colvars: # hardLowerBoundary = on
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = on
colvars: # outputAppliedForce = on
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: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group1" defined, 4 atoms initialized: total mass = 0.
colvars: Initializing atom group "group2".
colvars: # indexGroup = "" [default]
colvars: # psfSegID = [default]
colvars: # atomsFile = "" [default]
colvars: # dummyAtom = ( 0 , 0 , 0 ) [default]
colvars: # enableForces = on [default]
colvars: # disableForces = off [default]
colvars: # centerReference = off [default]
colvars: # rotateReference = off [default]
colvars: # enableFitGradients = on [default]
colvars: Atom group "group2" defined, 1 atoms initialized: total mass = 0.
colvars: All components initialized.
colvars: # width = 1 [default]
colvars: # lowerBoundary = 0
colvars: # lowerWallConstant = 0 [default]
colvars: # upperBoundary = 20
colvars: # upperWallConstant = 0 [default]
colvars: # hardLowerBoundary = on
colvars: # hardUpperBoundary = off [default]
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = on
colvars: # outputAppliedForce = on
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 2 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "abf" instance.
colvars: # name = abf
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # applyBias = off
colvars: WARNING: ABF biases will *not* be applied!
colvars: # updateBias = on [default]
colvars: # hideJacobian = off [default]
colvars: Jacobian (geometric) forces will be included in reported free energy gradients.
colvars: # fullSamples = 200 [default]
colvars: # inputPrefix = [default]
colvars: # outputFreq = 1000 [default]
colvars: # historyFreq = 0 [default]
colvars: # shared = off [default]
colvars: # maxForce = [default]
colvars: Finished ABF setup.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "histogram" instance.
colvars: # name = histo
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: # outputfreq = 1000 [default]
colvars: Finished histogram setup.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "metadynamics" instance.
colvars: # name = meta
colvars: # colvars = { one, two }
colvars: # outputEnergy = off [default]
colvars: Warning: running ABF and metadynamics together is not recommended unless applyBias is off for ABF.
colvars: # hillWeight = 0.01
colvars: # newHillFrequency = 1000 [default]
colvars: # hillWidth = 1.25331 [default]
colvars: # multipleReplicas = off [default]
colvars: # useGrids = on [default]
colvars: # gridsUpdateFrequency = 1000 [default]
colvars: # rebinGrids = off [default]
colvars: # keepHills = off [default]
colvars: # writeFreeEnergyFile = on [default]
colvars: # saveFreeEnergyFile = off [default]
colvars: # writeHillsTrajectory = off [default]
colvars: # wellTempered = off [default]
colvars: # biasTemperature = -1 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 3 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "out.colvars.state".
colvars: Restarting collective variable "one" from value: 10.8019
colvars: Restarting collective variable "two" from value: 8.37106
colvars: Restarting ABF bias "abf".
colvars: Restarting collective variable histogram "histo".
colvars: Restarting metadynamics bias "meta".
colvars: ----------------------------------------------------------------------
colvars: The restart output state file will be "rest.colvars.state".
colvars: The final output state file will be "out2.colvars.state".
colvars: Writing to colvar trajectory file "out2.colvars.traj".
colvars: Initializing step number as firstTimestep.
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 1 atoms: total mass = 12.011.
colvars: Re-initialized atom group two:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group two:0/1. 1 atoms: total mass = 12.011.
colvars: Prepared sample and gradient buffers at step 200.
colvars: Histogram histo will be written to file "out2.histo.dat"
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.87411e-06
6 0.996999 3.05638e-06
8 1.08 1.82265e-06
10 1.111 1.92009e-06
12 1.08 1.96521e-06
14 0.959999 0
18 0.9572 1.13163e-05
31 104.52 0.00114656
Memory usage per processor = 14.8029 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
200 280.25149 -5323.7989 -6451.2787 1127.4798 -6532.4552 19.301584 0.0022862156
210 264.04399 -5333.6176 -6395.893 1062.2754 -6472.9627 13.555607 0.0022862156
220 262.35164 -5342.4112 -6397.8781 1055.4669 -6483.5339 20.671671 0.00015177801
230 265.06522 -5347.6593 -6414.0432 1066.3839 -6495.628 16.286994 0.00015177801
240 269.66936 -5347.3649 -6432.2717 1084.9068 -6514.156 18.975841 0.00015177801
250 261.50997 -5341.964 -6394.0448 1052.0807 -6474.9399 16.007102 0.00015177801
260 267.13834 -5336.0104 -6410.7346 1074.7242 -6493.6451 14.702163 0.00015177801
270 271.46801 -5329.5747 -6421.7177 1092.1429 -6499.8101 20.348477 0.00015177801
280 278.54246 -5318.4599 -6439.0641 1120.6042 -6529.346 27.52287 0.00015177801
290 283.40941 -5306.7992 -6446.9836 1140.1844 -6529.7918 15.038254 0.0022862156
SHAKE stats (type/ave/delta) on step 300
4 1.111 2.95239e-07
6 0.997 8.76713e-07
8 1.08 1.06378e-06
10 1.111 1.34087e-06
12 1.08 7.69835e-07
14 0.96 0
18 0.957201 4.3509e-06
31 104.52 0.000409147
300 274.74107 -5299.7239 -6405.0346 1105.3108 -6481.7288 20.379233 0.0022862156
Loop time of 1.06301 on 2 procs for 100 steps with 2004 atoms
99.4% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 16.256 ns/day 1.476 hours/ns 94.072 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.81579 | 0.8195 | 0.82321 | 0.4 | 77.09
Bond | 0.002522 | 0.00266 | 0.0027981 | 0.3 | 0.25
Kspace | 0.093284 | 0.096691 | 0.1001 | 1.1 | 9.10
Neigh | 0.094059 | 0.094065 | 0.09407 | 0.0 | 8.85
Comm | 0.017479 | 0.017852 | 0.018225 | 0.3 | 1.68
Output | 0.00023055 | 0.0003289 | 0.00042725 | 0.5 | 0.03
Modify | 0.029282 | 0.02935 | 0.029417 | 0.0 | 2.76
Other | | 0.002561 | | | 0.24
Nlocal: 1002 ave 1004 max 1000 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8704 ave 8720 max 8688 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354168 ave 359537 max 348799 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708336
Ave neighs/atom = 353.461
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
colvars: Saving collective variables state to "out2.colvars.state".
colvars: Resetting the Collective Variables Module.
Please see the log.cite file for references relevant to this simulation
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