forked from lijiext/lammps
97 lines
3.3 KiB
Groff
97 lines
3.3 KiB
Groff
LAMMPS (5 Oct 2007)
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# Rhodopsin model
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units real
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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.rhodo
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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 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 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0
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special_bonds charmm
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thermo 50
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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 = 0.245875
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grid = 24 32 30
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RMS precision = 8.76365e-05
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brick FFT buffer size/proc = 12180 6144 5481
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Memory usage per processor = 50.2175 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -25355.8260 KinEng = 21444.8313 Temp = 299.0397
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PotEng = -46800.6573 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 = 203820.0665 E_long = -267197.5267 Press = -142.0485
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Volume = 307995.0335
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---------------- Step 50 ----- CPU = 9.6422 (sec) ----------------
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TotEng = -25329.9165 KinEng = 21500.9586 Temp = 299.8223
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PotEng = -46830.8752 E_bond = 2471.7583 E_angle = 10836.5458
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E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9667
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E_coul = 203591.3235 E_long = -267204.3691 Press = 238.4820
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Volume = 308031.8242
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---------------- Step 100 ----- CPU = 19.4814 (sec) ----------------
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TotEng = -25291.5443 KinEng = 21589.5406 Temp = 301.0576
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PotEng = -46881.0849 E_bond = 2568.0538 E_angle = 10781.7478
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E_dihed = 5198.3743 E_impro = 216.6829 E_vdwl = -1898.4506
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E_coul = 203451.2690 E_long = -267198.7621 Press = 10.7475
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Volume = 308134.7686
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Loop time of 19.4821 on 4 procs for 100 steps with 32000 atoms
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Pair time (%) = 12.9977 (66.7161)
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Bond time (%) = 0.64311 (3.30104)
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Kspce time (%) = 2.5143 (12.9057)
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Neigh time (%) = 1.95058 (10.0122)
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Comm time (%) = 0.480013 (2.46387)
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Outpt time (%) = 0.0015353 (0.00788057)
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Other time (%) = 0.894842 (4.59316)
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FFT time (% of Kspce) = 0.315807 (12.5604)
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FFT Gflps 3d 1d-only = 1.46568 6.19563
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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: 22735.5 ave 22770 max 22697 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Neighs: 3.00699e+06 ave 3.0975e+06 max 2.96494e+06 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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Total # of neighbors = 12027976
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Ave neighs/atom = 375.874
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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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