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lammps/examples/USER/colvars/log.peptide.colvars2
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log.peptide.colvars2
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LAMMPS (5 Mar 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)
2 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.colvars2
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) = 0.268721
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 = 2744 512 2352
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2012-03-03.
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, 4 initialized: total mass = 15.035.
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: # forceConstant = 100
colvars: # centers = { 10 }
colvars: # targetCenters = { 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 = 9.38576 Mbytes
Step Temp TotEng PotEng KinEng E_pair E_bond 2
0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 273.74323
10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269
20 309.56974 -4999.4935 -6244.9235 1245.43 -6401.697 43.595449 13.004392
30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
40 297.5581 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676872 25.625156
50 296.80003 -5117.2927 -6311.3489 1194.0562 -6451.8275 30.631279 5.3320296
60 281.72797 -5188.494 -6321.9138 1133.4198 -6427.8833 26.287652 20.573959
70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742889 0.69414877
80 268.01458 -5281.8502 -6360.0996 1078.2494 -6496.6063 20.300731 5.260643
90 270.43386 -5334.0847 -6422.0671 1087.9825 -6563.2487 39.845992 1.1832492
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 2.92453e-05
31 104.52 0.00239929
100 260.3562 -5387.2264 -6434.6654 1047.439 -6534.1924 20.24674 0.075048745
colvars: Saving collective variables state to "out.colvars.state".
Loop time of 0.419409 on 8 procs for 100 steps with 2004 atoms
Pair time (%) = 0.243947 (58.1644)
Bond time (%) = 0.00104892 (0.250095)
Kspace time (%) = 0.0674721 (16.0874)
Neigh time (%) = 0.0437018 (10.4199)
Comm time (%) = 0.0280269 (6.68247)
Output time (%) = 0.00782087 (1.86474)
Modify time (%) = 0.024282 (5.78958)
Other time (%) = 0.00310966 (0.74144)
FFT time (% of Kspce) = 0.00900686 (13.349)
FFT Gflps 3d (1d only) = 6.08847 19.2233
Nlocal: 250.5 ave 263 max 237 min
Histogram: 1 1 0 0 2 1 0 1 1 1
Nghost: 4934.75 ave 4960 max 4894 min
Histogram: 1 0 0 0 2 0 1 2 1 1
Neighs: 88529.1 ave 92368 max 83606 min
Histogram: 1 1 0 1 1 0 1 0 1 2
Total # of neighbors = 708233
Ave neighs/atom = 353.41
Ave special neighs/atom = 2.34032
Neighbor list builds = 13
Dangerous builds = 1
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