130 lines
4.6 KiB
Groff
130 lines
4.6 KiB
Groff
LAMMPS (9 Oct 2020)
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using 1 OpenMP thread(s) per MPI task
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# Rhodopsin model
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units real
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neighbor 2.0 bin
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neigh_modify delay 5 every 1
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atom_style full
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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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pair_style lj/charmm/coul/long 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm 1e-4
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read_data data.protein
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Reading data file ...
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orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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32000 atoms
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reading velocities ...
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32000 velocities
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scanning bonds ...
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4 = max bonds/atom
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scanning angles ...
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8 = max angles/atom
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scanning dihedrals ...
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18 = max dihedrals/atom
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scanning impropers ...
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2 = max impropers/atom
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reading bonds ...
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27723 bonds
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reading angles ...
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40467 angles
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reading dihedrals ...
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56829 dihedrals
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reading impropers ...
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1034 impropers
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0.0 0.0 0.0
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special bond factors coul: 0.0 0.0 0.0
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4 = max # of 1-2 neighbors
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12 = max # of 1-3 neighbors
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24 = max # of 1-4 neighbors
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26 = max # of special neighbors
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special bonds CPU = 0.011 seconds
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read_data CPU = 0.125 seconds
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fix 1 all shake 0.0001 5 0 m 1.0 a 232
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1617 = # of size 2 clusters
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3633 = # of size 3 clusters
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747 = # of size 4 clusters
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4233 = # of frozen angles
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find clusters CPU = 0.006 seconds
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fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
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special_bonds charmm
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thermo_style multi
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timestep 2.0
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:328)
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G vector (1/distance) = 0.24883488
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grid = 25 32 32
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stencil order = 5
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estimated absolute RMS force accuracy = 0.035547797
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estimated relative force accuracy = 0.00010705113
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using double precision KISS FFT
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3d grid and FFT values/proc = 41070 25600
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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 = 10 13 13
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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/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 140.0 | 140.0 | 140.0 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
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PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
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E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
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E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
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Volume = 307995.0335
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---------------- Step 100 ----- CPU = 20.0022 (sec) ----------------
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TotEng = -25290.7304 KinEng = 21591.9084 Temp = 301.0906
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PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571
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E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618
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E_coul = 206659.5226 E_long = -270404.9730 Press = 6.7406
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Volume = 308134.2285
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Loop time of 20.0022 on 1 procs for 100 steps with 32000 atoms
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Performance: 0.864 ns/day, 27.781 hours/ns, 4.999 timesteps/s
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99.9% CPU use with 1 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 | 15 | 15 | 15 | 0.0 | 74.99
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Bond | 0.65091 | 0.65091 | 0.65091 | 0.0 | 3.25
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Kspace | 1.2144 | 1.2144 | 1.2144 | 0.0 | 6.07
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Neigh | 2.6096 | 2.6096 | 2.6096 | 0.0 | 13.05
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Comm | 0.035203 | 0.035203 | 0.035203 | 0.0 | 0.18
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Output | 0.00010848 | 0.00010848 | 0.00010848 | 0.0 | 0.00
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Modify | 0.48116 | 0.48116 | 0.48116 | 0.0 | 2.41
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Other | | 0.01032 | | | 0.05
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Nlocal: 32000.0 ave 32000 max 32000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 47958.0 ave 47958 max 47958 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 12028093
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Ave neighs/atom = 375.87791
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Ave special neighs/atom = 7.4318750
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Neighbor list builds = 11
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Dangerous builds = 0
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Total wall time: 0:00:20
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