195 lines
7.2 KiB
Groff
195 lines
7.2 KiB
Groff
LAMMPS (27 Jun 2024)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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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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Reading data file ...
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orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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2004 atoms
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reading velocities ...
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2004 velocities
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scanning bonds ...
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3 = max bonds/atom
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scanning angles ...
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6 = max angles/atom
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scanning dihedrals ...
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14 = max dihedrals/atom
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scanning impropers ...
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1 = max impropers/atom
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orthogonal box = (36.840194 41.013691 29.768095) to (64.21156 68.385058 57.139462)
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1 by 2 by 2 MPI processor grid
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reading bonds ...
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1365 bonds
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reading angles ...
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786 angles
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reading dihedrals ...
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207 dihedrals
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reading impropers ...
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12 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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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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special bonds CPU = 0.000 seconds
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read_data CPU = 0.010 seconds
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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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fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0
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fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0
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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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Finding SHAKE clusters ...
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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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find clusters CPU = 0.000 seconds
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#dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz
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#dump_modify 1 sort id
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variable sp equal f_3a+f_3b
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thermo_style custom step temp etotal pe ke epair ebond v_sp
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thermo 10
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run 100
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
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@Article{Gissinger24,
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author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
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title = {Type Label Framework for Bonded Force Fields in LAMMPS},
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journal = {J. Phys. Chem. B},
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year = 2024,
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volume = 128,
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number = 13,
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pages = {3282–-3297}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.26872465
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grid = 15 15 15
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stencil order = 5
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estimated absolute RMS force accuracy = 0.022820853
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estimated relative force accuracy = 6.872432e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 4312 960
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Generated 91 of 91 mixed pair_coeff terms from arithmetic mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 5 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 5 5 5
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/charmm/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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SHAKE stats (type/ave/delta/count) on step 0
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Bond: 4 1.111 1.44264e-05 9
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Bond: 6 0.996998 7.26967e-06 6
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Bond: 8 1.08 1.32536e-05 7
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Bond: 10 1.111 1.22749e-05 8
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Bond: 12 1.08 1.11767e-05 9
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Bond: 14 0.96 0 1
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Bond: 18 0.957206 4.37979e-05 1280
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Angle: 31 104.519 0.00396029 640
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Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.22 | 16.41 Mbytes
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Step Temp TotEng PotEng KinEng E_pair E_bond v_sp
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0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604
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10 305.06149 -5058.8972 -6286.1901 1227.2929 -6413.1021 58.8499 103.38345
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20 311.00516 -4999.0612 -6250.266 1251.2048 -6417.1021 47.695297 36.699695
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30 314.22337 -4993.7012 -6257.8532 1264.152 -6421.9679 35.344144 10.563933
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40 297.87491 -5020.8378 -6219.2184 1198.3805 -6389.8528 27.723133 3.8354517
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50 304.02071 -5056.2576 -6279.3633 1223.1057 -6456.8214 55.459505 0.20678217
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60 285.92576 -5104.0461 -6254.354 1150.3079 -6435.5814 32.767229 0.69352945
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70 277.83519 -5163.9758 -6281.7345 1117.7587 -6447.7033 39.627168 11.433603
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80 267.51495 -5206.4046 -6282.644 1076.2394 -6456.6369 31.611883 6.3554178
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90 278.15579 -5245.3824 -6364.431 1119.0485 -6499.8063 28.849773 0.36941576
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SHAKE stats (type/ave/delta/count) on step 100
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Bond: 4 1.11098 8.97155e-05 9
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Bond: 6 0.996996 1.00568e-05 6
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Bond: 8 1.08 6.02345e-06 7
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Bond: 10 1.111 1.84253e-05 8
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Bond: 12 1.08 7.2713e-06 9
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Bond: 14 0.959996 0 1
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Bond: 18 0.957198 3.36079e-05 1280
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Angle: 31 104.52 0.0030599 640
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100 260.10613 -5292.6885 -6339.1215 1046.433 -6471.6734 25.362042 0.21987323
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Loop time of 0.247541 on 4 procs for 100 steps with 2004 atoms
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Performance: 69.806 ns/day, 0.344 hours/ns, 403.973 timesteps/s, 809.561 katom-step/s
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99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.17778 | 0.18129 | 0.18529 | 0.8 | 73.24
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Bond | 0.00024025 | 0.00049912 | 0.00080235 | 0.0 | 0.20
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Kspace | 0.016204 | 0.0204 | 0.023648 | 2.3 | 8.24
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Neigh | 0.032425 | 0.032462 | 0.032496 | 0.0 | 13.11
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Comm | 0.0063955 | 0.0065509 | 0.0067449 | 0.2 | 2.65
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Output | 0.0001675 | 0.00018071 | 0.00021385 | 0.0 | 0.07
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Modify | 0.0057027 | 0.0057304 | 0.0057568 | 0.0 | 2.31
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Other | | 0.0004289 | | | 0.17
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Nlocal: 501 ave 513 max 489 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Nghost: 6563.25 ave 6596 max 6519 min
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Histogram: 1 0 1 0 0 0 0 0 0 2
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Neighs: 177059 ave 181742 max 172942 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Total # of neighbors = 708237
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Ave neighs/atom = 353.41168
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Ave special neighs/atom = 2.3403194
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Neighbor list builds = 12
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Dangerous builds = 2
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Total wall time: 0:00:00
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