forked from lijiext/lammps
118 lines
3.7 KiB
Groff
118 lines
3.7 KiB
Groff
LAMMPS (5 Oct 2007)
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# Rhodopsin model
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variable x index 1
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variable y index 1
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variable z index 1
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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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atom_modify map hash
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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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replicate $x $y $z
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replicate 2 $y $z
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replicate 2 2 $z
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replicate 2 2 1
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orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615)
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2 by 2 by 1 processor grid
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128000 atoms
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110892 bonds
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161868 angles
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227316 dihedrals
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4136 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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6468 = # of size 2 clusters
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14532 = # of size 3 clusters
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2988 = # of size 4 clusters
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16932 = # 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 = 0.246338
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grid = 45 60 36
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RMS precision = 8.56639e-05
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brick FFT buffer size/proc = 40180 24840 17220
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Memory usage per processor = 137.911 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -101423.5112 KinEng = 85779.3251 Temp = 299.0304
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PotEng = -187202.8364 E_bond = 10151.9760 E_angle = 43685.4968
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E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4538
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E_coul = 817284.2513 E_long = -1070794.2991 Press = -141.9925
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Volume = 1231980.1340
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---------------- Step 50 ----- CPU = 38.9431 (sec) ----------------
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TotEng = -101316.6996 KinEng = 86004.2667 Temp = 299.8145
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PotEng = -187320.9663 E_bond = 9887.1225 E_angle = 43346.5775
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E_dihed = 20958.7139 E_impro = 908.4248 E_vdwl = -7973.9399
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E_coul = 816372.0088 E_long = -1070819.8739 Press = 238.0995
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Volume = 1232127.0570
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---------------- Step 100 ----- CPU = 79.6546 (sec) ----------------
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TotEng = -101158.1182 KinEng = 86360.5576 Temp = 301.0566
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PotEng = -187518.6758 E_bond = 10272.2506 E_angle = 43128.8182
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E_dihed = 20794.4833 E_impro = 867.0824 E_vdwl = -7591.0566
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E_coul = 815810.2886 E_long = -1070800.5424 Press = 13.1624
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Volume = 1232538.4006
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Loop time of 79.6554 on 4 procs for 100 steps with 128000 atoms
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Pair time (%) = 54.0019 (67.7944)
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Bond time (%) = 2.60068 (3.26491)
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Kspce time (%) = 9.92803 (12.4637)
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Neigh time (%) = 8.09826 (10.1666)
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Comm time (%) = 1.17806 (1.47895)
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Outpt time (%) = 0.00191575 (0.00240505)
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Other time (%) = 3.84657 (4.82902)
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FFT time (% of Kspce) = 1.57698 (15.8841)
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FFT Gflps 3d 1d-only = 1.41574 5.85277
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Nlocal: 32000 ave 32001 max 31999 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 47957.5 ave 47959 max 47956 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 1.2028e+07 ave 1.20576e+07 max 1.19984e+07 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 48112030
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Ave neighs/atom = 375.875
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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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