LAMMPS (16 Mar 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
  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
  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_style    multi
timestep        2.0

run		100
PPPM initialization ...
  using 12-bit tables for long-range coulomb (../kspace.cpp:321)
  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 ...
  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) = 49.07 | 49.17 | 49.46 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 =      6.3997 (sec) ----------------
TotEng   =    -25290.7386 KinEng   =     21591.9096 Temp     =       301.0906 
PotEng   =    -46882.6483 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 6.39977 on 4 procs for 100 steps with 32000 atoms

Performance: 2.700 ns/day, 8.889 hours/ns, 15.626 timesteps/s
98.8% CPU use with 4 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 4.4434     | 4.5321     | 4.6846     |   4.3 | 70.82
Bond    | 0.17894    | 0.18568    | 0.19951    |   1.9 |  2.90
Kspace  | 0.4651     | 0.61064    | 0.69123    |  11.1 |  9.54
Neigh   | 0.7739     | 0.77394    | 0.774      |   0.0 | 12.09
Comm    | 0.057676   | 0.069183   | 0.07901    |   3.0 |  1.08
Output  | 5.6505e-05 | 6.6578e-05 | 9.4414e-05 |   0.0 |  0.00
Modify  | 0.21444    | 0.21866    | 0.22524    |   0.9 |  3.42
Other   |            | 0.009451   |            |       |  0.15

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: 0:00:06
