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 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 (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 = 237705 184320 Memory usage per processor = 760.048 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 157024.0524 KinEng = 172792.6155 Temp = 301.1796 PotEng = -15768.5631 E_bond = 28164.9917 E_angle = 117224.0742 E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6324 E_coul = 1894295.6653 E_long = -2130488.8032 Press = 9562.1554 Volume = 2457390.7959 ---------------- Step 100 ----- CPU = 36.9731 (sec) ---------------- TotEng = -233301.5647 KinEng = 123222.8702 Temp = 214.7790 PotEng = -356524.4350 E_bond = 13098.4680 E_angle = 56766.9162 E_dihed = 45556.8237 E_impro = 1313.9365 E_vdwl = -40863.9296 E_coul = 1705084.9441 E_long = -2137481.5939 Press = -1634.3724 Volume = 2522232.6324 ---------------- Step 200 ----- CPU = 71.7796 (sec) ---------------- TotEng = -308341.5902 KinEng = 108937.0512 Temp = 189.8786 PotEng = -417278.6414 E_bond = 9579.0189 E_angle = 47373.5018 E_dihed = 39847.3805 E_impro = 967.6494 E_vdwl = -23632.3384 E_coul = 1646631.2737 E_long = -2138045.1272 Press = -1185.5582 Volume = 2554682.9557 Loop time of 71.7796 on 1 procs for 200 steps with 256000 atoms Pair time (%) = 10.4771 (14.5962) Bond time (%) = 27.3962 (38.1671) Kspce time (%) = 7.23529 (10.0799) Neigh time (%) = 5.6228 (7.83343) Comm time (%) = 0.678451 (0.945186) Outpt time (%) = 0.001441 (0.00200754) Other time (%) = 20.3683 (28.3762) FFT time (% of Kspce) = 5.21147 (72.0284) FFT Gflps 3d (1d only) = 1.71528 2.99119 Nlocal: 256000 ave 256000 max 256000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 161665 ave 161665 max 161665 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