LAMMPS (1 Feb 2014) # Rhodopsin model 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 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 1 by 1 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 4 = max bonds/atom scanning angles ... 8 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 2 = 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 fix 1 all shake 0.0001 5 0 m 1.0 a 232 1617 = # of size 2 clusters 3633 = # of size 3 clusters 747 = # of size 4 clusters 4233 = # 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 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector (1/distance) = 0.248835 grid = 25 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0355478 estimated relative force accuracy = 0.000107051 using double precision FFTs 3d grid and FFT values/proc = 41070 25600 Memory usage per processor = 139.238 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035 Volume = 307995.0335 ---------------- Step 50 ----- CPU = 17.8100 (sec) ---------------- TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230 PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975 E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754 E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701 Volume = 308031.5639 ---------------- Step 100 ----- CPU = 36.2348 (sec) ---------------- TotEng = -25290.7592 KinEng = 21592.0117 Temp = 301.0920 PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408 E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783 E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960 Volume = 308133.9888 Loop time of 36.2348 on 1 procs for 100 steps with 32000 atoms Pair time (%) = 26.0418 (71.8696) Bond time (%) = 1.26644 (3.4951) Kspce time (%) = 3.24933 (8.96742) Neigh time (%) = 4.47968 (12.3629) Comm time (%) = 0.0700378 (0.193289) Outpt time (%) = 0.000230074 (0.000634953) Other time (%) = 1.12729 (3.11108) FFT time (% of Kspce) = 0.276809 (8.51896) FFT Gflps 3d (1d only) = 1.87746 3.23903 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 47958 ave 47958 max 47958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12028107 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0