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lammps/examples/USER/colvars/log.peptide-colvars2
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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 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 peptide2.colvars.*"
fix 2 all colvars peptide.colvars2 output peptide2
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.colvar2.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 2014-10-26.
colvars: Using LAMMPS interface, version 2014-10-26.
colvars: ----------------------------------------------------------------------
colvars: Reading new configuration from file "peptide.colvars2":
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, 4 atoms initialized: total mass = 0.
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, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = h_pot
colvars: # colvars = { one }
colvars: # outputEnergy = off [default]
colvars: # forceConstant = 100
colvars: # centers = { 10 }
colvars: # targetCenters = { 10 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: # outputCenters = off [default]
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 "peptide2.colvars.state".
colvars: Writing to colvar trajectory file "peptide2.colvars.traj".
colvars: Re-initialized atom group one:0/0. 4 atoms: total mass = 15.035.
colvars: Re-initialized atom group one:0/1. 4 atoms: total mass = 15.035.
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 273.74323
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154
50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302
60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8834 26.28765 20.573958
70 277.26045 -5224.8415 -6340.288 1115.4465 -6447.8494 27.742889 0.69414895
80 268.01458 -5281.8501 -6360.0995 1078.2495 -6496.6062 20.300729 5.260642
90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249
SHAKE stats (type/ave/delta) on step 100
4 1.11096 0.000191466
6 0.996989 3.5552e-05
8 1.08 9.10001e-06
10 1.111 1.58547e-05
12 1.08 5.80613e-06
14 0.959997 0
18 0.957198 2.92454e-05
31 104.52 0.00239929
100 260.35617 -5387.2297 -6434.6686 1047.4389 -6534.1956 20.246734 0.075048996
Loop time of 1.09685 on 2 procs for 100 steps with 2004 atoms
99.1% CPU use with 2 MPI tasks x 1 OpenMP threads
Performance: 15.754 ns/day 1.523 hours/ns 91.170 timesteps/s
MPI task timings breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.79732 | 0.80134 | 0.80536 | 0.4 | 73.06
Bond | 0.0024555 | 0.002741 | 0.0030265 | 0.5 | 0.25
Kspace | 0.090389 | 0.095391 | 0.10039 | 1.6 | 8.70
Neigh | 0.15028 | 0.15029 | 0.15029 | 0.0 | 13.70
Comm | 0.017451 | 0.018635 | 0.019819 | 0.9 | 1.70
Output | 0.00022626 | 0.00031698 | 0.0004077 | 0.5 | 0.03
Modify | 0.025696 | 0.025744 | 0.025793 | 0.0 | 2.35
Other | | 0.002393 | | | 0.22
Nlocal: 1002 ave 1010 max 994 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 8645 ave 8652 max 8638 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 354116 ave 356373 max 351860 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 708233
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
colvars: Saving collective variables state to "peptide2.colvars.state".
colvars: Resetting the Collective Variables Module.
Please see the log.cite file for references relevant to this simulation
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