LAMMPS (29 Jun 2012)
# 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
  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

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 ...
  G vector (1/distance) = 0.248831
  grid = 25 32 32
  stencil order = 5
  estimated absolute RMS force accuracy = 0.025142
  estimated relative force accuracy = 7.57143e-05
  using double precision FFTs
  brick FFT buffer size/proc = 13230 6400 5670
Memory usage per processor = 54.5952 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =    -25356.2055 KinEng   =     21444.8313 Temp     =       299.0397 
PotEng   =    -46801.0368 E_bond   =      2537.9940 E_angle  =     10921.3742 
E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
E_coul   =    207021.6603 E_long   =   -270399.5000 Press    =      -142.6030 
Volume   =    307995.0335 
---------------- Step      100 ----- CPU =      9.8819 (sec) ----------------
TotEng   =    -25290.7642 KinEng   =     21592.0080 Temp     =       301.0920 
PotEng   =    -46882.7722 E_bond   =      2567.9806 E_angle  =     10781.9408 
E_dihed  =      5198.7431 E_impro  =       216.7832 E_vdwl   =     -1902.4804 
E_coul   =    206654.9995 E_long   =   -270400.7390 Press    =         6.9875 
Volume   =    308133.9900 
Loop time of 9.88193 on 4 procs for 100 steps with 32000 atoms

Pair  time (%) = 6.69935 (67.794)
Bond  time (%) = 0.326266 (3.30164)
Kspce time (%) = 1.20454 (12.1893)
Neigh time (%) = 1.14156 (11.552)
Comm  time (%) = 0.0931967 (0.943103)
Outpt time (%) = 7.80225e-05 (0.000789547)
Other time (%) = 0.416932 (4.21914)

FFT time (% of Kspce) = 0.0984144 (8.17028)
FFT Gflps 3d (1d only) = 5.28071 12.3682

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:    3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1

Total # of neighbors = 12028107
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
