forked from lijiext/lammps
136 lines
4.1 KiB
Groff
136 lines
4.1 KiB
Groff
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LAMMPS (1 Feb 2014)
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# Rhodopsin model
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newton off
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package gpu force/neigh 0 1 1
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variable x index 2
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variable y index 2
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variable z index 2
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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/gpu 8.0 10.0
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pair_modify mix arithmetic
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kspace_style pppm/gpu 1e-4
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read_data data.rhodo
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orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
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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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18 = max angles/atom
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scanning dihedrals ...
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40 = max dihedrals/atom
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scanning impropers ...
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4 = 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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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 2
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orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
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1 by 1 by 1 MPI processor grid
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256000 atoms
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221784 bonds
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323736 angles
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454632 dihedrals
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8272 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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12936 = # of size 2 clusters
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29064 = # of size 3 clusters
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5976 = # of size 4 clusters
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33864 = # 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 100
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thermo_style multi
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timestep 2.0
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run 200
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PPPM initialization ...
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G vector (1/distance) = 0.245959
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grid = 48 64 60
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stencil order = 5
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estimated absolute RMS force accuracy = 0.0410392
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estimated relative force accuracy = 0.000123588
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using double precision FFTs
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3d grid and FFT values/proc = 237705 184320
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Memory usage per processor = 760.048 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
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PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
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E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
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E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
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Volume = 2457390.7959
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---------------- Step 100 ----- CPU = 36.3779 (sec) ----------------
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TotEng = -233301.6813 KinEng = 123222.9259 Temp = 214.7790
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PotEng = -356524.6072 E_bond = 13098.4672 E_angle = 56766.9111
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E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
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E_coul = 1705084.7672 E_long = -2137481.5867 Press = -1634.3912
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Volume = 2522232.6302
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---------------- Step 200 ----- CPU = 70.7784 (sec) ----------------
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TotEng = -308342.0030 KinEng = 108937.4160 Temp = 189.8792
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PotEng = -417279.4189 E_bond = 9579.0134 E_angle = 47373.6274
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E_dihed = 39847.4817 E_impro = 967.6755 E_vdwl = -23635.2960
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E_coul = 1646633.4711 E_long = -2138045.3918 Press = -1185.9327
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Volume = 2554683.1533
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Loop time of 70.7784 on 1 procs for 200 steps with 256000 atoms
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Pair time (%) = 10.0374 (14.1815)
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Bond time (%) = 27.2471 (38.4963)
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Kspce time (%) = 7.19169 (10.1608)
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Neigh time (%) = 5.43951 (7.68527)
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Comm time (%) = 0.681534 (0.962912)
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Outpt time (%) = 0.00139809 (0.0019753)
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Other time (%) = 20.1798 (28.5112)
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FFT time (% of Kspce) = 5.17983 (72.0253)
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FFT Gflps 3d (1d only) = 1.72575 2.95071
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Nlocal: 256000 ave 256000 max 256000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 161662 ave 161662 max 161662 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 0 ave 0 max 0 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 0
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Ave neighs/atom = 0
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Ave special neighs/atom = 7.43187
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Neighbor list builds = 31
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Dangerous builds = 12
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Please see the log.cite file for references relevant to this simulation
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