LAMMPS (18 Feb 2013) # 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 (1/distance) = 0.245959 grid = 48 64 60 stencil order = 5 estimated absolute RMS force accuracy = 0.0410392 estimated relative force accuracy = 0.000123588 using double precision FFTs 3d grid and FFT values/proc = 68635 46080 Memory usage per processor = 250.358 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 157024.0492 KinEng = 172792.6155 Temp = 301.1796 PotEng = -15768.5663 E_bond = 28164.9917 E_angle = 117224.0742 E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324 E_coul = 1894295.6622 E_long = -2130488.8032 Press = 9562.1554 Volume = 2457390.7959 ---------------- Step 100 ----- CPU = 12.1280 (sec) ---------------- TotEng = -233301.6590 KinEng = 123222.8183 Temp = 214.7789 PotEng = -356524.4772 E_bond = 13098.4683 E_angle = 56766.9228 E_dihed = 45556.8211 E_impro = 1313.9369 E_vdwl = -40863.9000 E_coul = 1705084.8591 E_long = -2137481.5855 Press = -1634.3808 Volume = 2522232.6313 ---------------- Step 200 ----- CPU = 23.3169 (sec) ---------------- TotEng = -308342.2597 KinEng = 108936.8553 Temp = 189.8783 PotEng = -417279.1150 E_bond = 9579.0042 E_angle = 47373.6037 E_dihed = 39847.3737 E_impro = 967.6451 E_vdwl = -23631.6382 E_coul = 1646630.1738 E_long = -2138045.2773 Press = -1185.5491 Volume = 2554682.9808 Loop time of 23.3169 on 4 procs for 200 steps with 256000 atoms Pair time (%) = 4.29395 (18.4156) Bond time (%) = 6.57406 (28.1944) Kspce time (%) = 4.75311 (20.3848) Neigh time (%) = 1.32057 (5.66359) Comm time (%) = 0.555436 (2.38212) Outpt time (%) = 0.000431776 (0.00185177) Other time (%) = 5.81936 (24.9577) FFT time (% of Kspce) = 1.78333 (37.5192) FFT Gflps 3d (1d only) = 5.0126 11.639 Nlocal: 64000 ave 64003 max 63997 min Histogram: 1 0 0 1 0 0 1 0 0 1 Nghost: 70636.8 ave 70640 max 70632 min Histogram: 1 0 0 0 0 0 1 1 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