Homec4science
Diffusion lammps (lammps-icms) Browse

lammps/examples/USER/colvars/log.peptide-abf
a8a95efae3e7lammps-icms

Last Change
Raw File

log.peptide-abf
View Options

LAMMPS (21 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 1 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.abf 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 = 10648 3375
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2014-10-24.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.abf":
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 = on
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: Collective variables biases initialized, 1 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.
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 = 15.1551 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
10 277.56202 -5234.5267 -6351.1865 1116.6598 -6421.6673 15.157737 0
20 279.23914 -5226.3715 -6349.7785 1123.407 -6438.893 20.182593 0
30 282.18508 -5222.2101 -6357.4689 1135.2588 -6447.4787 20.633694 0
40 275.79415 -5220.6026 -6330.15 1109.5474 -6418.1917 12.957903 0
50 285.29502 -5218.0696 -6365.8399 1147.7704 -6444.236 16.49252 0
60 271.80932 -5220.1144 -6313.6305 1093.5161 -6406.0186 20.082649 0
70 273.78833 -5224.3654 -6325.8432 1101.4778 -6411.4835 20.116139 0
80 273.59878 -5228.1218 -6328.837 1100.7152 -6417.5929 17.278957 0
90 285.1598 -5229.7433 -6376.9697 1147.2264 -6462.8871 25.416574 0
SHAKE stats (type/ave/delta) on step 100
4 1.111 1.94821e-06
6 0.996999 1.95513e-06
8 1.08 1.31363e-06
10 1.111 1.50162e-06
12 1.08 7.11588e-07
14 0.959999 0
18 0.9572 9.09672e-06
31 104.52 0.000738832
100 271.72303 -5234.6676 -6327.8364 1093.1689 -6417.4309 16.436681 0
Loop time of 2.26058 on 1 procs for 100 steps with 2004 atoms
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 7.644 ns/day 3.140 hours/ns 44.236 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8211 | 1.8211 | 1.8211 | 0.0 | 80.56
Bond | 0.0052092 | 0.0052092 | 0.0052092 | 0.0 | 0.23
Kspace | 0.18822 | 0.18822 | 0.18822 | 0.0 | 8.33
Neigh | 0.20887 | 0.20887 | 0.20887 | 0.0 | 9.24
Comm | 0.0097327 | 0.0097327 | 0.0097327 | 0.0 | 0.43
Output | 0.00024152 | 0.00024152 | 0.00024152 | 0.0 | 0.01
Modify | 0.024986 | 0.024986 | 0.024986 | 0.0 | 1.11
Other | | 0.002172 | | | 0.10
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11138 ave 11138 max 11138 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708038 ave 708038 max 708038 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708038
Ave neighs/atom = 353.312
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 = 10648 3375
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 1.95513e-06
8 1.08 1.31363e-06
10 1.111 1.50162e-06
12 1.08 7.11588e-07
14 0.959999 0
18 0.9572 9.09672e-06
31 104.52 0.000738832
Memory usage per processor = 15.1551 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
100 271.72303 -5234.6676 -6327.8364 1093.1689 -6417.4309 16.436681 0
110 282.16131 -5238.8524 -6374.0155 1135.1632 -6468.973 26.409952 0
120 279.45401 -5243.5466 -6367.818 1124.2714 -6463.8618 26.02577 0
130 271.89469 -5252.2317 -6346.0912 1093.8595 -6438.0037 17.493788 0
140 272.07731 -5263.1495 -6357.7437 1094.5942 -6448.0536 24.576321 0
150 273.22917 -5275.1404 -6374.3687 1099.2283 -6457.5303 20.61675 0
160 283.33338 -5284.0726 -6423.9511 1139.8785 -6508.5175 17.881775 0
170 276.87524 -5293.0365 -6406.9333 1113.8968 -6497.0038 18.80942 0
180 276.52856 -5304.8136 -6417.3157 1112.5021 -6498.7829 18.007541 0
190 274.63469 -5315.0171 -6419.8999 1104.8828 -6500.9028 13.341442 0
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.87471e-06
6 0.996999 3.05704e-06
8 1.08 1.82303e-06
10 1.111 1.92003e-06
12 1.08 1.967e-06
14 0.959999 0
18 0.9572 1.13191e-05
31 104.52 0.00114646
200 280.26317 -5323.8117 -6451.3385 1127.5268 -6532.4914 19.303399 0
Loop time of 2.28263 on 1 procs for 100 steps with 2004 atoms
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 7.570 ns/day 3.170 hours/ns 43.809 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8381 | 1.8381 | 1.8381 | 0.0 | 80.53
Bond | 0.0052245 | 0.0052245 | 0.0052245 | 0.0 | 0.23
Kspace | 0.19121 | 0.19121 | 0.19121 | 0.0 | 8.38
Neigh | 0.21067 | 0.21067 | 0.21067 | 0.0 | 9.23
Comm | 0.0097909 | 0.0097909 | 0.0097909 | 0.0 | 0.43
Output | 0.00026798 | 0.00026798 | 0.00026798 | 0.0 | 0.01
Modify | 0.025167 | 0.025167 | 0.025167 | 0.0 | 1.10
Other | | 0.00217 | | | 0.10
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11133 ave 11133 max 11133 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 707934 ave 707934 max 707934 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 707934
Ave neighs/atom = 353.26
Ave special neighs/atom = 2.34032
Neighbor list builds = 8
Dangerous builds = 0
fix 2 all colvars peptide.abf 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 = 10648 3375
colvars: Creating proxy instance
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2014-10-24.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.abf":
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 = on
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: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Collective variables module (re)initialized.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "out.colvars.state".
colvars: Restarting collective variable "one" from value: 10.8015
colvars: Restarting collective variable "two" from value: 8.37052
colvars: Restarting ABF bias "abf".
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.
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.87471e-06
6 0.996999 3.05704e-06
8 1.08 1.82303e-06
10 1.111 1.92003e-06
12 1.08 1.967e-06
14 0.959999 0
18 0.9572 1.13191e-05
31 104.52 0.00114646
Memory usage per processor = 15.1551 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
200 280.26317 -5323.8117 -6451.3385 1127.5268 -6532.4914 19.303399 0
210 264.04128 -5333.6349 -6395.8994 1062.2645 -6472.9679 13.551822 0
220 262.34335 -5342.4338 -6397.8673 1055.4335 -6483.528 20.662868 0
230 265.06475 -5347.6936 -6414.0756 1066.382 -6495.647 16.284978 0
240 269.68528 -5347.4019 -6432.3727 1084.9708 -6514.2601 18.979765 0
250 261.51604 -5342.0061 -6394.1113 1052.1052 -6475.0058 16.005204 0
260 267.18447 -5336.0534 -6410.9633 1074.9098 -6493.8355 14.695191 0
270 271.46038 -5329.6471 -6421.7593 1092.1122 -6499.8468 20.34702 0
280 278.55746 -5318.5412 -6439.2058 1120.6645 -6529.477 27.51316 0
290 283.34044 -5306.9019 -6446.8088 1139.9069 -6529.6115 15.039805 0
SHAKE stats (type/ave/delta) on step 300
4 1.111 2.96478e-07
6 0.997 8.75896e-07
8 1.08 1.05442e-06
10 1.111 1.33748e-06
12 1.08 7.69484e-07
14 0.96 0
18 0.957201 4.31577e-06
31 104.52 0.000408944
300 274.78038 -5299.7629 -6405.2319 1105.4689 -6481.9007 20.367754 0
Loop time of 2.28692 on 1 procs for 100 steps with 2004 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Performance: 7.556 ns/day 3.176 hours/ns 43.727 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.8432 | 1.8432 | 1.8432 | 0.0 | 80.60
Bond | 0.005337 | 0.005337 | 0.005337 | 0.0 | 0.23
Kspace | 0.18967 | 0.18967 | 0.18967 | 0.0 | 8.29
Neigh | 0.21109 | 0.21109 | 0.21109 | 0.0 | 9.23
Comm | 0.010032 | 0.010032 | 0.010032 | 0.0 | 0.44
Output | 0.00026464 | 0.00026464 | 0.00026464 | 0.0 | 0.01
Modify | 0.025214 | 0.025214 | 0.025214 | 0.0 | 1.10
Other | | 0.002144 | | | 0.09
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11260 ave 11260 max 11260 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708321 ave 708321 max 708321 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708321
Ave neighs/atom = 353.454
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
c4science · Help