LAMMPS (9 Oct 2020) using 1 OpenMP thread(s) per MPI task # Rhodopsin model units real neighbor 2.0 bin 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.protein Reading data file ... orthogonal box = (-27.500000 -38.500000 -36.364600) to (27.500000 38.500000 36.361500) 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 Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0.0 0.0 0.0 special bond factors coul: 0.0 0.0 0.0 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors special bonds CPU = 0.005 seconds read_data CPU = 0.210 seconds 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 find clusters CPU = 0.003 seconds 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_style multi timestep 2.0 run 100 PPPM initialization ... using 12-bit tables for long-range coulomb (src/kspace.cpp:328) G vector (1/distance) = 0.24883488 grid = 25 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.035547797 estimated relative force accuracy = 0.00010705113 using double precision KISS FFT 3d grid and FFT values/proc = 13230 6400 Neighbor list info ... 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 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 49.25 | 49.35 | 49.64 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 100 ----- CPU = 5.5375 (sec) ---------------- TotEng = -25290.7303 KinEng = 21591.9085 Temp = 301.0906 PotEng = -46882.6388 E_bond = 2567.9807 E_angle = 10781.9571 E_dihed = 5198.7492 E_impro = 216.7864 E_vdwl = -1902.6618 E_coul = 206659.5225 E_long = -270404.9730 Press = 6.7406 Volume = 308134.2285 Loop time of 5.53765 on 4 procs for 100 steps with 32000 atoms Performance: 3.120 ns/day, 7.691 hours/ns, 18.058 timesteps/s 99.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8921 | 3.9427 | 4.0762 | 3.9 | 71.20 Bond | 0.16218 | 0.16829 | 0.17972 | 1.7 | 3.04 Kspace | 0.35196 | 0.48475 | 0.53996 | 11.1 | 8.75 Neigh | 0.69975 | 0.69981 | 0.69988 | 0.0 | 12.64 Comm | 0.04908 | 0.049445 | 0.049767 | 0.1 | 0.89 Output | 5.1737e-05 | 8.5056e-05 | 0.00018382 | 0.0 | 0.00 Modify | 0.18393 | 0.18474 | 0.18528 | 0.1 | 3.34 Other | | 0.007858 | | | 0.14 Nlocal: 8000.00 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 = 12028093 Ave neighs/atom = 375.87791 Ave special neighs/atom = 7.4318750 Neighbor list builds = 11 Dangerous builds = 0 Total wall time: 0:00:05