LAMMPS (6 Oct 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 ... WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316) 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 = 37.3604 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 = -149.3301 Volume = 307995.0335 ---------------- Step 50 ----- CPU = 4.6056 (sec) ---------------- TotEng = -25330.0321 KinEng = 21501.0036 Temp = 299.8230 PotEng = -46831.0357 E_bond = 2471.7033 E_angle = 10836.5108 E_dihed = 5239.6316 E_impro = 227.1219 E_vdwl = -1993.2763 E_coul = 206797.6655 E_long = -270410.3927 Press = 237.6866 Volume = 308031.5640 ---------------- Step 100 ----- CPU = 9.3910 (sec) ---------------- TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906 PotEng = -46882.6482 E_bond = 2567.9789 E_angle = 10781.9556 E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458 E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898 Volume = 308133.9933 Loop time of 9.39107 on 4 procs for 100 steps with 32000 atoms Performance: 1.840 ns/day, 13.043 hours/ns, 10.648 timesteps/s 99.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2189 | 6.3266 | 6.6072 | 6.5 | 67.37 Bond | 0.30793 | 0.32122 | 0.3414 | 2.4 | 3.42 Kspace | 0.87994 | 1.1644 | 1.2855 | 15.3 | 12.40 Neigh | 1.1358 | 1.136 | 1.1362 | 0.0 | 12.10 Comm | 0.08292 | 0.084935 | 0.087077 | 0.5 | 0.90 Output | 0.00015712 | 0.00016558 | 0.00018501 | 0.1 | 0.00 Modify | 0.33717 | 0.34246 | 0.34794 | 0.7 | 3.65 Other | | 0.01526 | | | 0.16 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: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min Histogram: 1 2 0 0 0 0 0 0 0 1 Total # of neighbors = 12028098 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 Total wall time: 0:00:09