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 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 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 = 0.011 seconds read_data CPU = 0.125 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 = 0.006 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 = 41070 25600 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) = 140.0 | 140.0 | 140.0 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 = 20.0022 (sec) ---------------- TotEng = -25290.7304 KinEng = 21591.9084 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 = 206659.5226 E_long = -270404.9730 Press = 6.7406 Volume = 308134.2285 Loop time of 20.0022 on 1 procs for 100 steps with 32000 atoms Performance: 0.864 ns/day, 27.781 hours/ns, 4.999 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15 | 15 | 15 | 0.0 | 74.99 Bond | 0.65091 | 0.65091 | 0.65091 | 0.0 | 3.25 Kspace | 1.2144 | 1.2144 | 1.2144 | 0.0 | 6.07 Neigh | 2.6096 | 2.6096 | 2.6096 | 0.0 | 13.05 Comm | 0.035203 | 0.035203 | 0.035203 | 0.0 | 0.18 Output | 0.00010848 | 0.00010848 | 0.00010848 | 0.0 | 0.00 Modify | 0.48116 | 0.48116 | 0.48116 | 0.0 | 2.41 Other | | 0.01032 | | | 0.05 Nlocal: 32000.0 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 47958.0 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 = 12028093 Ave neighs/atom = 375.87791 Ave special neighs/atom = 7.4318750 Neighbor list builds = 11 Dangerous builds = 0 Total wall time: 0:00:20