forked from lijiext/lammps
517 lines
22 KiB
Plaintext
517 lines
22 KiB
Plaintext
LAMMPS (21 May 2012-ICMS)
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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3 = max bonds/atom
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6 = max angles/atom
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14 = max dihedrals/atom
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1 = max impropers/atom
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 1 by 1 MPI processor grid
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2004 atoms
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2004 velocities
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1365 bonds
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786 angles
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207 dihedrals
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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group peptide type <= 12
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84 atoms in group peptide
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group one id 2 4 5 6
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4 atoms in group one
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group two id 80 82 83 84
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4 atoms in group two
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group ref id 37
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1 atoms in group ref
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group colvar union one two ref
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9 atoms in group colvar
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fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
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shell "rm -f out*.colvars.*"
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fix 2 all colvars peptide.colvars
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fix 2a ref setforce 0.0 0.0 0.0
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fix 4 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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#dump 1 colvar custom 1 dump.colvar.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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thermo_style custom step temp etotal pe ke epair ebond f_2
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thermo 10
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run 100
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PPPM initialization ...
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G vector (1/distance) = 0.268721
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.01614
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estimated relative force accuracy = 4.86052e-05
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using single precision FFTs
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brick FFT buffer size/proc = 10648 3375 5808
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colvars: ----------------------------------------------------------------------
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colvars: Initializing the collective variables module, version 2012-03-23.
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colvars: # analysis = off [default]
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colvars: # colvarsTrajFrequency = 1
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colvars: # colvarsRestartFrequency = 1000
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colvars: # colvarsTrajAppend = off [default]
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colvars: The restart output state file will be "rest.colvars.state".
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colvars: The final output state file will be "out.colvars.state".
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colvars: The trajectory file will be "out.colvars.traj".
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = one
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colvars: Initializing a new "distance" component.
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # oneSiteSystemForce = off [default]
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colvars: Initializing atom group "group1".
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colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
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colvars: Initializing atom group "group2".
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colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
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colvars: All components initialized.
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # lowerWallConstant = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # upperWallConstant = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputSystemForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = two
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colvars: Initializing a new "distance" component.
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # oneSiteSystemForce = off [default]
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colvars: Initializing atom group "group1".
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colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
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colvars: Initializing atom group "group2".
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colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
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colvars: All components initialized.
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # lowerWallConstant = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # upperWallConstant = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputSystemForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables initialized, 2 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new "harmonic" instance.
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colvars: # name = h_pot
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colvars: # colvars = { one, two }
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colvars: # forceConstant = 100
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colvars: # centers = { 10, 10 }
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colvars: # targetCenters = { 10, 10 } [default]
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colvars: # targetForceConstant = 0 [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables biases initialized, 1 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables module initialized.
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colvars: ----------------------------------------------------------------------
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Memory usage per processor = 22.5866 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond 2
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0 282.10052 -5237.458 -6372.3765 1134.9186 -6442.7679 16.557152 292.14604
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10 305.06198 -5058.8899 -6286.1847 1227.2948 -6413.0967 58.849896 103.38344
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20 311.00592 -4999.0544 -6250.2623 1251.2079 -6417.0984 47.695274 36.699706
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30 314.22398 -4993.6953 -6257.8498 1264.1545 -6421.9643 35.344163 10.563914
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40 297.87524 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.723201 3.8354392
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50 304.02086 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459508 0.20679801
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60 285.92594 -5104.0436 -6254.3523 1150.3086 -6435.5793 32.76729 0.69356508
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70 277.835 -5163.9752 -6281.7332 1117.758 -6447.7015 39.627148 11.433632
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80 267.51473 -5206.4042 -6282.6427 1076.2385 -6456.6352 31.611843 6.3553235
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90 278.15513 -5245.383 -6364.4289 1119.0459 -6499.8037 28.849899 0.36938867
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SHAKE stats (type/ave/delta) on step 100
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4 1.11098 8.97184e-05
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6 0.996996 1.00568e-05
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8 1.08 6.02345e-06
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10 1.111 1.84257e-05
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12 1.08 7.27136e-06
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14 0.959996 0
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18 0.957198 3.36077e-05
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31 104.52 0.00306008
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100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
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colvars: Saving collective variables state to "out.colvars.state".
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Loop time of 2.39102 on 1 procs for 100 steps with 2004 atoms
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Pair time (%) = 1.86583 (78.0347)
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Bond time (%) = 0.00628591 (0.262896)
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Kspace time (%) = 0.165128 (6.90614)
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Neigh time (%) = 0.314792 (13.1656)
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Comm time (%) = 0.0111108 (0.464687)
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Output time (%) = 0.000252724 (0.0105697)
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Modify time (%) = 0.0253747 (1.06125)
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Other time (%) = 0.0022521 (0.0941899)
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FFT time (% of Kspce) = 0.0274372 (16.6158)
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FFT Gflps 3d (1d only) = 1.99867 2.86506
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Nlocal: 2004 ave 2004 max 2004 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11124 ave 11124 max 11124 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 708237 ave 708237 max 708237 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 708237
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Ave neighs/atom = 353.412
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 12
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Dangerous builds = 2
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run 100
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PPPM initialization ...
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G vector (1/distance) = 0.268721
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.01614
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estimated relative force accuracy = 4.86052e-05
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using single precision FFTs
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brick FFT buffer size/proc = 10648 3375 5808
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colvars: ----------------------------------------------------------------------
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colvars: Initializing the collective variables module, version 2012-03-23.
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colvars: # analysis = off [default]
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colvars: # colvarsTrajFrequency = 1
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colvars: # colvarsRestartFrequency = 1000
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colvars: # colvarsTrajAppend = off [default]
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colvars: The restart output state file will be "rest.colvars.state".
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colvars: The final output state file will be "out.colvars.state".
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colvars: The trajectory file will be "out.colvars.traj".
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = one
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colvars: Initializing a new "distance" component.
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # oneSiteSystemForce = off [default]
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colvars: Initializing atom group "group1".
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colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
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colvars: Initializing atom group "group2".
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colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
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colvars: All components initialized.
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # lowerWallConstant = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # upperWallConstant = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputSystemForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = two
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colvars: Initializing a new "distance" component.
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # oneSiteSystemForce = off [default]
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colvars: Initializing atom group "group1".
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colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
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colvars: Initializing atom group "group2".
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colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
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colvars: All components initialized.
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # lowerWallConstant = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # upperWallConstant = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputSystemForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables initialized, 2 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new "harmonic" instance.
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colvars: # name = h_pot
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colvars: # colvars = { one, two }
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colvars: # forceConstant = 100
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colvars: # centers = { 10, 10 }
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colvars: # targetCenters = { 10, 10 } [default]
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colvars: # targetForceConstant = 0 [default]
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables biases initialized, 1 in total.
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colvars: ----------------------------------------------------------------------
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colvars: Restarting from file "out.colvars.state".
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colvars: Restarting collective variable "one" from value: 10.0137
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colvars: Restarting collective variable "two" from value: 10.0649
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colvars: Restarting harmonic bias "h_pot".
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colvars: Reading current stage from the restart.
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colvars: # stage = 3900175693153042431
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colvars: ----------------------------------------------------------------------
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colvars: Collective variables module initialized.
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colvars: ----------------------------------------------------------------------
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colvars: Initializing step number as firstTimestep.
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SHAKE stats (type/ave/delta) on step 100
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4 1.11098 8.97184e-05
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6 0.996996 1.00568e-05
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8 1.08 6.02345e-06
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10 1.111 1.84257e-05
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12 1.08 7.27136e-06
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14 0.959996 0
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18 0.957198 3.36077e-05
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31 104.52 0.00306008
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Memory usage per processor = 22.5866 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond 2
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100 260.10505 -5292.6892 -6339.1178 1046.4286 -6471.6694 25.361885 0.2198687
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110 266.26278 -5341.2103 -6412.412 1071.2018 -6552.7583 33.572968 1.9229782
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120 262.66442 -5386.2494 -6442.9746 1056.7252 -6587.5499 29.859553 2.7124877
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130 252.8344 -5422.5446 -6439.7226 1017.1781 -6580.4752 25.979049 1.2031628
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140 253.85115 -5452.1905 -6473.4591 1021.2686 -6609.489 26.071514 0.30586247
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150 261.31825 -5490.48 -6541.7895 1051.3095 -6646.6144 16.258548 6.9049974
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160 255.7368 -5521.6048 -6550.4596 1028.8547 -6658.1517 19.717533 12.339821
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170 253.42877 -5540.1003 -6559.6695 1019.5693 -6656.6878 23.293662 10.289878
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180 248.51086 -5550.3244 -6550.1084 999.78404 -6661.4182 26.200056 3.4339065
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190 250.8039 -5555.2614 -6564.2706 1009.0092 -6666.15 25.536594 3.3495152
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 1.8129e-06
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6 0.997 7.7964e-07
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8 1.08 1.08934e-06
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10 1.111 2.96501e-07
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12 1.08 4.69174e-07
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14 0.960001 0
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18 0.957201 3.76571e-06
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31 104.52 0.000411068
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200 251.50581 -5557.4209 -6569.2539 1011.833 -6674.0867 24.805164 7.1388858
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colvars: Saving collective variables state to "out.colvars.state".
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Loop time of 2.23495 on 1 procs for 100 steps with 2004 atoms
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Pair time (%) = 1.84544 (82.572)
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Bond time (%) = 0.00609159 (0.27256)
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Kspace time (%) = 0.163201 (7.30223)
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Neigh time (%) = 0.183405 (8.20622)
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Comm time (%) = 0.00959301 (0.429227)
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Output time (%) = 0.000245094 (0.0109664)
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Modify time (%) = 0.0247326 (1.10663)
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Other time (%) = 0.00223875 (0.10017)
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FFT time (% of Kspce) = 0.0272989 (16.7271)
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FFT Gflps 3d (1d only) = 2.0088 2.93901
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Nlocal: 2004 ave 2004 max 2004 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 11159 ave 11159 max 11159 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 708088 ave 708088 max 708088 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 708088
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Ave neighs/atom = 353.337
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 7
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Dangerous builds = 0
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fix 2 all colvars peptide.colvars input out.colvars.state output out2
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run 100
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PPPM initialization ...
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G vector (1/distance) = 0.268721
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.01614
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estimated relative force accuracy = 4.86052e-05
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using single precision FFTs
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brick FFT buffer size/proc = 10648 3375 5808
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colvars: ----------------------------------------------------------------------
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colvars: Initializing the collective variables module, version 2012-03-23.
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colvars: # analysis = off [default]
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colvars: # colvarsTrajFrequency = 1
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colvars: # colvarsRestartFrequency = 1000
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colvars: # colvarsTrajAppend = off [default]
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colvars: The restart output state file will be "rest.colvars.state".
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colvars: The final output state file will be "out2.colvars.state".
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colvars: The trajectory file will be "out2.colvars.traj".
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = one
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colvars: Initializing a new "distance" component.
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colvars: # componentCoeff = 1 [default]
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colvars: # componentExp = 1 [default]
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colvars: # period = 0 [default]
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colvars: # wrapAround = 0 [default]
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colvars: # forceNoPBC = off [default]
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colvars: # oneSiteSystemForce = off [default]
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colvars: Initializing atom group "group1".
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colvars: Atom group "group1" defined, 4 initialized: total mass = 15.035.
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colvars: Initializing atom group "group2".
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colvars: Atom group "group2" defined, 1 initialized: total mass = 12.011.
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colvars: All components initialized.
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colvars: # width = 1 [default]
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colvars: # lowerBoundary = 0 [default]
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colvars: # lowerWallConstant = 0 [default]
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colvars: # upperBoundary = 0 [default]
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colvars: # upperWallConstant = 0 [default]
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colvars: # expandBoundaries = off [default]
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colvars: # extendedLagrangian = off [default]
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colvars: # outputValue = on [default]
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colvars: # outputVelocity = off [default]
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colvars: # outputSystemForce = off [default]
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colvars: # outputAppliedForce = off [default]
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colvars: ----------------------------------------------------------------------
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colvars: Initializing a new collective variable.
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colvars: # name = two
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colvars: Initializing a new "distance" component.
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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
|
|
|