LAMMPS (15 Feb 2016) # 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 2 by 2 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 = 13230 6400 Neighbor list info ... 1 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6 -> bins = 10 13 13 Memory usage per processor = 36.629 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 = 4.7461 (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 = 9.6332 (sec) ---------------- TotEng = -25290.7591 KinEng = 21592.0117 Temp = 301.0920 PotEng = -46882.7708 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 9.63322 on 4 procs for 100 steps with 32000 atoms Performance: 1.794 ns/day, 13.379 hours/ns, 10.381 timesteps/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4364 | 6.5993 | 6.7208 | 4.7 | 68.51 Bond | 0.30755 | 0.32435 | 0.35704 | 3.4 | 3.37 Kspace | 0.92248 | 1.0782 | 1.2597 | 13.0 | 11.19 Neigh | 1.1669 | 1.1672 | 1.1675 | 0.0 | 12.12 Comm | 0.094674 | 0.098065 | 0.10543 | 1.4 | 1.02 Output | 0.00015521 | 0.00016224 | 0.00018215 | 0.1 | 0.00 Modify | 0.32982 | 0.34654 | 0.35365 | 1.6 | 3.60 Other | | 0.01943 | | | 0.20 Nlocal: 8000 ave 8143 max 7933 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 22733.5 ave 22769 max 22693 min Histogram: 1 0 0 0 0 2 0 0 0 1 Neighs: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min Histogram: 1 2 0 0 0 0 0 0 0 1 Total # of neighbors = 12028107 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 Total wall time: 0:00:10