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
