LAMMPS (6 Oct 2016) # Rhodopsin model variable x index 1 variable y index 1 variable z index 1 units real neigh_modify delay 5 every 1 atom_style full atom_modify map hash 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 replicate $x $y $z replicate 2 $y $z replicate 2 2 $z replicate 2 2 1 orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615) 2 by 2 by 1 MPI processor grid 128000 atoms 110892 bonds 161868 angles 227316 dihedrals 4136 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 6468 = # of size 2 clusters 14532 = # of size 3 clusters 2988 = # of size 4 clusters 16932 = # 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 ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) G vector (1/distance) = 0.248593 grid = 48 60 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0359793 estimated relative force accuracy = 0.00010835 using double precision FFTs 3d grid and FFT values/proc = 41615 25920 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 = 19 26 13 Memory usage per processor = 96.9597 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304 PotEng = -187204.8138 E_bond = 10151.9760 E_angle = 43685.4968 E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537 E_coul = 827053.5824 E_long = -1080565.6077 Press = -149.0358 Volume = 1231980.1340 ---------------- Step 50 ----- CPU = 18.1689 (sec) ---------------- TotEng = -101320.0211 KinEng = 86003.4933 Temp = 299.8118 PotEng = -187323.5144 E_bond = 9887.1189 E_angle = 43346.8448 E_dihed = 20958.7108 E_impro = 908.4721 E_vdwl = -7973.4486 E_coul = 826141.5493 E_long = -1080592.7617 Press = 238.0404 Volume = 1232126.1814 ---------------- Step 100 ----- CPU = 37.2027 (sec) ---------------- TotEng = -101157.9546 KinEng = 86355.7413 Temp = 301.0398 PotEng = -187513.6959 E_bond = 10272.0456 E_angle = 43128.7018 E_dihed = 20794.0107 E_impro = 867.0928 E_vdwl = -7587.2409 E_coul = 825584.2416 E_long = -1080572.5474 Press = 15.1729 Volume = 1232535.8440 Loop time of 37.2028 on 4 procs for 100 steps with 128000 atoms Performance: 0.464 ns/day, 51.671 hours/ns, 2.688 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 | 25.431 | 25.738 | 25.984 | 4.0 | 69.18 Bond | 1.2966 | 1.3131 | 1.3226 | 0.9 | 3.53 Kspace | 3.7563 | 4.0123 | 4.3127 | 10.0 | 10.79 Neigh | 4.3778 | 4.378 | 4.3782 | 0.0 | 11.77 Comm | 0.1903 | 0.19549 | 0.20485 | 1.3 | 0.53 Output | 0.00031805 | 0.00037521 | 0.00039601 | 0.2 | 0.00 Modify | 1.4861 | 1.5051 | 1.5122 | 0.9 | 4.05 Other | | 0.05992 | | | 0.16 Nlocal: 32000 ave 32000 max 32000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 47957 ave 47957 max 47957 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 1.20281e+07 ave 1.20572e+07 max 1.19991e+07 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 48112540 Ave neighs/atom = 375.879 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 Total wall time: 0:00:38