forked from lijiext/lammps
94 lines
3.0 KiB
Groff
94 lines
3.0 KiB
Groff
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LAMMPS (29 Jun 2012)
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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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4 = max bonds/atom
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8 = max angles/atom
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18 = max dihedrals/atom
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2 = max impropers/atom
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orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
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1 by 2 by 2 MPI processor grid
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32000 atoms
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32000 velocities
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27723 bonds
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40467 angles
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56829 dihedrals
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1034 impropers
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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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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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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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G vector (1/distance) = 0.248831
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grid = 25 32 32
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stencil order = 5
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estimated absolute RMS force accuracy = 0.025142
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estimated relative force accuracy = 7.57143e-05
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using double precision FFTs
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brick FFT buffer size/proc = 13230 6400 5670
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Memory usage per processor = 54.5952 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
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PotEng = -46801.0368 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 = 207021.6603 E_long = -270399.5000 Press = -142.6030
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Volume = 307995.0335
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---------------- Step 100 ----- CPU = 9.8819 (sec) ----------------
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TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920
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PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408
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E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
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E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875
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Volume = 308133.9900
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Loop time of 9.88193 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 6.69935 (67.794)
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Bond time (%) = 0.326266 (3.30164)
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Kspce time (%) = 1.20454 (12.1893)
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Neigh time (%) = 1.14156 (11.552)
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Comm time (%) = 0.0931967 (0.943103)
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Outpt time (%) = 7.80225e-05 (0.000789547)
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Other time (%) = 0.416932 (4.21914)
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FFT time (% of Kspce) = 0.0984144 (8.17028)
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FFT Gflps 3d (1d only) = 5.28071 12.3682
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Nlocal: 8000 ave 8143 max 7933 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Nghost: 22733.5 ave 22769 max 22693 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 12028107
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Ave neighs/atom = 375.878
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Ave special neighs/atom = 7.43187
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Neighbor list builds = 11
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Dangerous builds = 0
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