LAMMPS (5 Oct 2007)
# 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 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 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 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 = 0.246338
  grid = 45 60 36
  RMS precision = 8.56639e-05
  brick FFT buffer size/proc = 40180 24840 17220
Memory usage per processor = 137.911 Mbytes
---------------- Step        0 ----- CPU =      0.0000 (sec) ----------------
TotEng   =   -101423.5112 KinEng   =     85779.3251 Temp     =       299.0304 
PotEng   =   -187202.8364 E_bond   =     10151.9760 E_angle  =     43685.4968 
E_dihed  =     20847.1460 E_impro  =       854.0463 E_vdwl   =     -9231.4538 
E_coul   =    817284.2513 E_long   =  -1070794.2991 Press    =      -141.9925 
Volume   =   1231980.1340 
---------------- Step       50 ----- CPU =     38.9431 (sec) ----------------
TotEng   =   -101316.6996 KinEng   =     86004.2667 Temp     =       299.8145 
PotEng   =   -187320.9663 E_bond   =      9887.1225 E_angle  =     43346.5775 
E_dihed  =     20958.7139 E_impro  =       908.4248 E_vdwl   =     -7973.9399 
E_coul   =    816372.0088 E_long   =  -1070819.8739 Press    =       238.0995 
Volume   =   1232127.0570 
---------------- Step      100 ----- CPU =     79.6546 (sec) ----------------
TotEng   =   -101158.1182 KinEng   =     86360.5576 Temp     =       301.0566 
PotEng   =   -187518.6758 E_bond   =     10272.2506 E_angle  =     43128.8182 
E_dihed  =     20794.4833 E_impro  =       867.0824 E_vdwl   =     -7591.0566 
E_coul   =    815810.2886 E_long   =  -1070800.5424 Press    =        13.1624 
Volume   =   1232538.4006 
Loop time of 79.6554 on 4 procs for 100 steps with 128000 atoms

Pair  time (%) = 54.0019 (67.7944)
Bond  time (%) = 2.60068 (3.26491)
Kspce time (%) = 9.92803 (12.4637)
Neigh time (%) = 8.09826 (10.1666)
Comm  time (%) = 1.17806 (1.47895)
Outpt time (%) = 0.00191575 (0.00240505)
Other time (%) = 3.84657 (4.82902)

FFT time (% of Kspce) = 1.57698 (15.8841)
FFT Gflps 3d 1d-only = 1.41574 5.85277

Nlocal:    32000 ave 32001 max 31999 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost:    47957.5 ave 47959 max 47956 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs:    1.2028e+07 ave 1.20576e+07 max 1.19984e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2

Total # of neighbors = 48112030
Ave neighs/atom = 375.875
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
