LAMMPS (7 Jul 2009)
# 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 2 by 2 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 300.0 300.0 100.0 		aniso NULL NULL NULL NULL 0.0 0.0 1000.0

special_bonds   charmm
 
thermo          50
thermo_style    multi 
timestep        2.0

run		100
PPPM initialization ...
  G vector = 0.248831
  grid = 25 32 32
  stencil order = 5
  RMS precision = 7.57143e-05
  brick FFT buffer size/proc = 13230 6400 5670
Memory usage per processor = 47.7552 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =    -25356.2081 KinEng   =     21444.8313 Temp     =       299.0397 
PotEng   =    -46801.0393 E_bond   =      2537.9940 E_angle  =     10921.3742 
E_dihed  =      5211.7865 E_impro  =       213.5116 E_vdwl   =     -2307.8634 
E_coul   =    207021.6578 E_long   =   -270399.5000 Press    =      -142.6055 
Volume   =    307995.0335 
---------------- Step       50 ----- CPU =      9.3409 (sec) ----------------
TotEng   =    -25330.0565 KinEng   =     21501.0002 Temp     =       299.8229 
PotEng   =    -46831.0567 E_bond   =      2471.7010 E_angle  =     10836.4978 
E_dihed  =      5239.6302 E_impro  =       227.1217 E_vdwl   =     -1993.2861 
E_coul   =    206793.4380 E_long   =   -270406.1593 Press    =       237.6633 
Volume   =    308031.6776 
---------------- Step      100 ----- CPU =     18.9741 (sec) ----------------
TotEng   =    -25290.7382 KinEng   =     21592.0112 Temp     =       301.0920 
PotEng   =    -46882.7494 E_bond   =      2567.9820 E_angle  =     10781.9426 
E_dihed  =      5198.7430 E_impro  =       216.7831 E_vdwl   =     -1902.4962 
E_coul   =    206655.0352 E_long   =   -270400.7391 Press    =         6.9485 
Volume   =    308134.2307 
Loop time of 18.9748 on 4 procs for 100 steps with 32000 atoms

Pair  time (%) = 12.4679 (65.7076)
Bond  time (%) = 0.674445 (3.55442)
Kspce time (%) = 2.50158 (13.1837)
Neigh time (%) = 1.93391 (10.192)
Comm  time (%) = 0.488374 (2.5738)
Outpt time (%) = 0.0020867 (0.0109972)
Other time (%) = 0.906525 (4.77751)

FFT time (% of Kspce) = 0.475504 (19.0082)
FFT Gflps 3d (1d only) = 1.09294 6.72748

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 2.96493e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1

Total # of neighbors = 12028097
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
