forked from lijiext/lammps
97 lines
3.3 KiB
Groff
97 lines
3.3 KiB
Groff
LAMMPS (22 June 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 1 by 1 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 = 37555 23040 11655
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Memory usage per processor = 134.779 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -25355.8254 KinEng = 21444.8313 Temp = 299.0397
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PotEng = -46800.6567 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 = 203820.0671 E_long = -267197.5267 Press = -142.0456
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Volume = 307995.0335
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---------------- Step 50 ----- CPU = 152.6104 (sec) ----------------
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TotEng = -25329.9175 KinEng = 21500.9583 Temp = 299.8223
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PotEng = -46830.8758 E_bond = 2471.7583 E_angle = 10836.5458
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E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9669
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E_coul = 203591.3230 E_long = -267204.3691 Press = 238.4815
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Volume = 308031.8243
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---------------- Step 100 ----- CPU = 309.5271 (sec) ----------------
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TotEng = -25291.5484 KinEng = 21589.5399 Temp = 301.0576
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PotEng = -46881.0883 E_bond = 2568.0537 E_angle = 10781.7480
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E_dihed = 5198.3744 E_impro = 216.6829 E_vdwl = -1898.4511
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E_coul = 203451.2661 E_long = -267198.7623 Press = 10.7451
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Volume = 308134.7692
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Loop time of 309.527 on 1 procs for 100 steps with 32000 atoms
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Pair time (%) = 231.215 (74.6994)
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Bond time (%) = 6.3242 (2.04318)
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Kspce time (%) = 19.1711 (6.19366)
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Neigh time (%) = 46.0779 (14.8865)
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Comm time (%) = 0.796922 (0.257464)
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Outpt time (%) = 0.002562 (0.000827714)
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Other time (%) = 5.93944 (1.91888)
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FFT time (% of Kspce) = 3.96566 (20.6857)
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FFT Gflps 3d 1d-only = 0.11672 0.259612
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Nlocal: 32000 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: 47962 ave 47962 max 47962 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.2028e+07 ave 1.2028e+07 max 1.2028e+07 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 12027978
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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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