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
