forked from lijiext/lammps
183 lines
6.7 KiB
Plaintext
183 lines
6.7 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 peptide2.colvars.*"
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fix 2 all colvars peptide.colvars2 output peptide2
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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.colvar2.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 "peptide2.colvars.state".
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colvars: The trajectory file will be "peptide2.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, 4 initialized: total mass = 15.035.
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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, 1 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 }
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colvars: # forceConstant = 100
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colvars: # centers = { 10 }
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colvars: # targetCenters = { 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 = 22.5865 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 273.74323
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10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.4169 21.367753 12.393269
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20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.697 43.595449 13.004392
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30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862
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40 297.5581 -5088.2156 -6285.3215 1197.106 -6395.3714 13.676872 25.625156
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50 296.80003 -5117.2926 -6311.3488 1194.0562 -6451.8274 30.631279 5.3320296
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60 281.72797 -5188.4941 -6321.9139 1133.4198 -6427.8834 26.287652 20.573958
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70 277.26045 -5224.8417 -6340.2882 1115.4465 -6447.8496 27.742888 0.69414894
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80 268.01458 -5281.8503 -6360.0997 1078.2494 -6496.6064 20.300731 5.2606438
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90 270.43386 -5334.0846 -6422.067 1087.9824 -6563.2486 39.845993 1.1832496
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SHAKE stats (type/ave/delta) on step 100
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4 1.11096 0.000191466
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6 0.996989 3.5552e-05
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8 1.08 9.1e-06
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10 1.111 1.58547e-05
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12 1.08 5.80613e-06
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14 0.959997 0
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18 0.957198 2.92453e-05
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31 104.52 0.00239929
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100 260.3562 -5387.2263 -6434.6653 1047.439 -6534.1923 20.24674 0.075048834
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colvars: Saving collective variables state to "peptide2.colvars.state".
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Loop time of 2.37975 on 1 procs for 100 steps with 2004 atoms
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Pair time (%) = 1.83713 (77.1984)
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Bond time (%) = 0.00636029 (0.267267)
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Kspace time (%) = 0.162295 (6.81981)
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Neigh time (%) = 0.336338 (14.1333)
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Comm time (%) = 0.0106671 (0.448243)
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Output time (%) = 0.000264168 (0.0111006)
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Modify time (%) = 0.024472 (1.02834)
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Other time (%) = 0.00222516 (0.0935038)
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FFT time (% of Kspce) = 0.028162 (17.3524)
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FFT Gflps 3d (1d only) = 1.94723 2.85015
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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: 11143 ave 11143 max 11143 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 708233 ave 708233 max 708233 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 708233
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Ave neighs/atom = 353.41
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 13
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Dangerous builds = 1
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