LAMMPS (1 Feb 2014) # 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 orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645) 1 by 2 by 2 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 4 = max bonds/atom scanning angles ... 18 = max angles/atom scanning dihedrals ... 40 = max dihedrals/atom scanning impropers ... 4 = max impropers/atom reading bonds ... 27723 bonds reading angles ... 40467 angles reading dihedrals ... 56829 dihedrals reading impropers ... 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 = 157024.0504 KinEng = 172792.6155 Temp = 301.1796 PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742 E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323 E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557 Volume = 2457390.7959 ---------------- Step 100 ----- CPU = 12.3409 (sec) ---------------- TotEng = -233301.6797 KinEng = 123222.9259 Temp = 214.7790 PotEng = -356524.6057 E_bond = 13098.4672 E_angle = 56766.9111 E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278 E_coul = 1705084.7688 E_long = -2137481.5867 Press = -1634.3910 Volume = 2522232.6302 ---------------- Step 200 ----- CPU = 23.6590 (sec) ---------------- TotEng = -308341.9699 KinEng = 108937.4196 Temp = 189.8792 PotEng = -417279.3895 E_bond = 9579.0134 E_angle = 47373.6274 E_dihed = 39847.4807 E_impro = 967.6755 E_vdwl = -23635.2996 E_coul = 1646633.5046 E_long = -2138045.3916 Press = -1185.9299 Volume = 2554683.1519 Loop time of 23.6591 on 4 procs for 200 steps with 256000 atoms Pair time (%) = 4.81669 (20.3587) Bond time (%) = 6.52579 (27.5826) Kspce time (%) = 4.48765 (18.968) Neigh time (%) = 1.3238 (5.5953) Comm time (%) = 0.490551 (2.07342) Outpt time (%) = 0.000454485 (0.00192098) Other time (%) = 6.01414 (25.42) FFT time (% of Kspce) = 1.77734 (39.6051) FFT Gflps 3d (1d only) = 5.02949 11.6654 Nlocal: 64000 ave 64001 max 63999 min Histogram: 1 0 0 0 0 2 0 0 0 1 Nghost: 70656.5 ave 70660 max 70654 min Histogram: 1 0 0 2 0 0 0 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 Please see the log.cite file for references relevant to this simulation