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 1 by 1 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 1 by 1 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 = 237705 184320 40365 Memory usage per processor = 757.714 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 157025.0401 KinEng = 172792.6155 Temp = 301.1796 PotEng = -15767.5754 E_bond = 28164.9917 E_angle = 117224.0742 E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324 E_coul = 1894235.3907 E_long = -2130427.5409 Press = 9562.2425 Volume = 2457390.7959 ---------------- Step 100 ----- CPU = 36.8336 (sec) ---------------- TotEng = -233301.4802 KinEng = 123222.6026 Temp = 214.7785 PotEng = -356524.0828 E_bond = 13098.4631 E_angle = 56766.9481 E_dihed = 45556.8121 E_impro = 1313.9420 E_vdwl = -40863.8988 E_coul = 1705023.3608 E_long = -2137419.7102 Press = -1634.3633 Volume = 2522232.7977 ---------------- Step 200 ----- CPU = 72.2618 (sec) ---------------- TotEng = -308340.6857 KinEng = 108944.3257 Temp = 189.8913 PotEng = -417285.0114 E_bond = 9579.0680 E_angle = 47373.8383 E_dihed = 39847.6180 E_impro = 967.6100 E_vdwl = -23634.8218 E_coul = 1646565.2623 E_long = -2137983.5863 Press = -1185.9778 Volume = 2554683.5150 Loop time of 72.2618 on 1 procs for 200 steps with 256000 atoms Pair time (%) = 10.1078 (13.9878) Bond time (%) = 29.9182 (41.4025) Kspce time (%) = 7.29844 (10.1) Neigh time (%) = 1.64225 (2.27264) Comm time (%) = 0.614946 (0.850997) Outpt time (%) = 0.00137877 (0.00190803) Other time (%) = 22.6787 (31.3841) FFT time (% of Kspce) = 5.23688 (71.7535) FFT Gflps 3d (1d only) = 1.70695 3.00498 Nlocal: 256000 ave 256000 max 256000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 161678 ave 161678 max 161678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 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