LAMMPS (14 Aug 2013)
# 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
  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 1 by 1 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

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 ...
  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 = 41070 25600
Memory usage per processor = 139.238 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    =      -142.6035 
Volume   =    307995.0335 
---------------- Step       50 ----- CPU =     17.7652 (sec) ----------------
TotEng   =    -25330.0828 KinEng   =     21501.0029 Temp     =       299.8230 
PotEng   =    -46831.0857 E_bond   =      2471.7004 E_angle  =     10836.4975 
E_dihed  =      5239.6299 E_impro  =       227.1218 E_vdwl   =     -1993.2754 
E_coul   =    206797.6331 E_long   =   -270410.3930 Press    =       237.6701 
Volume   =    308031.5639 
---------------- Step      100 ----- CPU =     36.1527 (sec) ----------------
TotEng   =    -25290.7592 KinEng   =     21592.0117 Temp     =       301.0920 
PotEng   =    -46882.7709 E_bond   =      2567.9807 E_angle  =     10781.9408 
E_dihed  =      5198.7432 E_impro  =       216.7834 E_vdwl   =     -1902.4783 
E_coul   =    206659.2327 E_long   =   -270404.9733 Press    =         6.9960 
Volume   =    308133.9888 
Loop time of 36.1528 on 1 procs for 100 steps with 32000 atoms

Pair  time (%) = 26.1216 (72.2533)
Bond  time (%) = 1.27574 (3.52875)
Kspce time (%) = 3.25689 (9.00869)
Neigh time (%) = 4.3025 (11.9009)
Comm  time (%) = 0.0688474 (0.190435)
Outpt time (%) = 0.000230074 (0.000636394)
Other time (%) = 1.127 (3.11732)

FFT time (% of Kspce) = 0.277417 (8.51784)
FFT Gflps 3d (1d only) = 1.87335 3.23863

Nlocal:    32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    47958 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 = 12028107
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
