LAMMPS (14 Aug 2013)
# 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
  4 = max bonds/atom
  8 = max angles/atom
  18 = max dihedrals/atom
  2 = max impropers/atom
  orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
  1 by 2 by 2 MPI processor grid
  32000 atoms
  32000 velocities
  27723 bonds
  40467 angles
  56829 dihedrals
  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 ...
  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
Memory usage per processor = 146.358 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    =      -142.3092 
Volume   =   1231980.1340 
---------------- Step       50 ----- CPU =     19.2151 (sec) ----------------
TotEng   =   -101320.2676 KinEng   =     86003.4837 Temp     =       299.8118 
PotEng   =   -187323.7514 E_bond   =      9887.1072 E_angle  =     43346.7922 
E_dihed  =     20958.7032 E_impro  =       908.4715 E_vdwl   =     -7973.4457 
E_coul   =    826141.3831 E_long   =  -1080592.7629 Press    =       238.0161 
Volume   =   1232126.1855 
---------------- Step      100 ----- CPU =     39.0436 (sec) ----------------
TotEng   =   -101158.1853 KinEng   =     86355.6148 Temp     =       301.0393 
PotEng   =   -187513.8001 E_bond   =     10272.0693 E_angle  =     43128.6453 
E_dihed  =     20793.9759 E_impro  =       867.0826 E_vdwl   =     -7586.7186 
E_coul   =    825583.7120 E_long   =  -1080572.5667 Press    =        15.2151 
Volume   =   1232535.8423 
Loop time of 39.0437 on 4 procs for 100 steps with 128000 atoms

Pair  time (%) = 27.1533 (69.546)
Bond  time (%) = 1.31501 (3.36805)
Kspce time (%) = 4.35908 (11.1646)
Neigh time (%) = 4.42268 (11.3275)
Comm  time (%) = 0.229435 (0.587637)
Outpt time (%) = 0.000313759 (0.00080361)
Other time (%) = 1.56382 (4.00532)

FFT time (% of Kspce) = 0.466478 (10.7013)
FFT Gflps 3d (1d only) = 5.13382 11.4048

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 1.1999e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 48112472
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
