LAMMPS (10 Jan 2012) # Rhodopsin model newton off package gpu force/neigh 0 1 1 variable x index 2 variable y index 2 variable z index 2 units real neigh_modify delay 5 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long/gpu 8.0 10.0 pair_modify mix arithmetic kspace_style pppm/gpu 1e-4 read_data data.rhodo 4 = max bonds/atom 18 = max angles/atom 40 = max dihedrals/atom 4 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645) 1 by 2 by 2 MPI processor grid 32000 atoms 32000 velocities 27723 bonds 40467 angles 56829 dihedrals 1034 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors replicate $x $y $z replicate 2 $y $z replicate 2 2 $z replicate 2 2 2 orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797) 1 by 2 by 2 MPI processor grid 256000 atoms 221784 bonds 323736 angles 454632 dihedrals 8272 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors fix 1 all shake 0.0001 5 0 m 1.0 a 232 12936 = # of size 2 clusters 29064 = # of size 3 clusters 5976 = # of size 4 clusters 33864 = # of frozen angles fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 100 thermo_style multi timestep 2.0 run 200 PPPM initialization ... G vector = 0.245952 grid = 48 64 60 stencil order = 5 RMS precision = 8.7421e-05 using double precision FFTs brick FFT buffer size/proc = 68635 46080 17649 Memory usage per processor = 249.821 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 157025.0390 KinEng = 172792.6155 Temp = 301.1796 PotEng = -15767.5765 E_bond = 28164.9917 E_angle = 117224.0742 E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324 E_coul = 1894235.3896 E_long = -2130427.5409 Press = 9562.2425 Volume = 2457390.7959 ---------------- Step 100 ----- CPU = 12.2605 (sec) ---------------- TotEng = -233301.4713 KinEng = 123222.6058 Temp = 214.7785 PotEng = -356524.0771 E_bond = 13098.4614 E_angle = 56766.9463 E_dihed = 45556.8096 E_impro = 1313.9414 E_vdwl = -40863.8548 E_coul = 1705023.3285 E_long = -2137419.7095 Press = -1634.3527 Volume = 2522232.7976 ---------------- Step 200 ----- CPU = 23.7724 (sec) ---------------- TotEng = -308340.7251 KinEng = 108941.9220 Temp = 189.8871 PotEng = -417282.6471 E_bond = 9579.0415 E_angle = 47373.9551 E_dihed = 39847.5174 E_impro = 967.5823 E_vdwl = -23636.2292 E_coul = 1646568.9776 E_long = -2137983.4917 Press = -1186.1181 Volume = 2554683.4248 Loop time of 23.7725 on 4 procs for 200 steps with 256000 atoms Pair time (%) = 4.55113 (19.1446) Bond time (%) = 7.43137 (31.2604) Kspce time (%) = 3.8699 (16.2789) Neigh time (%) = 0.51208 (2.15409) Comm time (%) = 0.544156 (2.28902) Outpt time (%) = 0.000452995 (0.00190555) Other time (%) = 6.86337 (28.8711) FFT time (% of Kspce) = 1.94085 (50.1524) FFT Gflps 3d (1d only) = 4.60577 11.8123 Nlocal: 64000 ave 64003 max 63997 min Histogram: 1 0 0 1 0 0 1 0 0 1 Nghost: 70640.8 ave 70645 max 70636 min Histogram: 1 0 0 0 1 0 1 0 0 1 Neighs: 0 ave 0 max 0 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0 Ave special neighs/atom = 7.43187 Neighbor list builds = 31 Dangerous builds = 12