mirror of https://github.com/lammps/lammps.git
118 lines
3.7 KiB
Groff
118 lines
3.7 KiB
Groff
LAMMPS (21 May 2008)
|
|
# 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 = 0.248586
|
|
grid = 48 60 36
|
|
RMS precision = 7.66425e-05
|
|
brick FFT buffer size/proc = 41615 25920 12915
|
|
Memory usage per processor = 130.497 Mbytes
|
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
|
TotEng = -101425.4928 KinEng = 85779.3251 Temp = 299.0304
|
|
PotEng = -187204.8179 E_bond = 10151.9760 E_angle = 43685.4968
|
|
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4538
|
|
E_coul = 827025.3455 E_long = -1080537.3748 Press = -142.3110
|
|
Volume = 1231980.1340
|
|
---------------- Step 50 ----- CPU = 36.7269 (sec) ----------------
|
|
TotEng = -101320.2392 KinEng = 86003.4766 Temp = 299.8118
|
|
PotEng = -187323.7158 E_bond = 9887.1093 E_angle = 43346.7930
|
|
E_dihed = 20958.7048 E_impro = 908.4715 E_vdwl = -7973.4918
|
|
E_coul = 826113.2245 E_long = -1080564.5270 Press = 237.9865
|
|
Volume = 1232126.6400
|
|
---------------- Step 100 ----- CPU = 75.0337 (sec) ----------------
|
|
TotEng = -101158.0378 KinEng = 86355.6419 Temp = 301.0394
|
|
PotEng = -187513.6797 E_bond = 10272.0762 E_angle = 43128.6553
|
|
E_dihed = 20793.9769 E_impro = 867.0831 E_vdwl = -7586.7842
|
|
E_coul = 825555.6424 E_long = -1080544.3294 Press = 15.1826
|
|
Volume = 1232536.8037
|
|
Loop time of 75.0342 on 4 procs for 100 steps with 128000 atoms
|
|
|
|
Pair time (%) = 51.7185 (68.9266)
|
|
Bond time (%) = 2.75642 (3.67355)
|
|
Kspce time (%) = 8.1762 (10.8966)
|
|
Neigh time (%) = 7.97927 (10.6342)
|
|
Comm time (%) = 0.971261 (1.29442)
|
|
Outpt time (%) = 0.00181103 (0.0024136)
|
|
Other time (%) = 3.43075 (4.57224)
|
|
|
|
FFT time (% of Kspce) = 1.65796 (20.2779)
|
|
FFT Gflps 3d 1d-only = 1.44443 6.12502
|
|
|
|
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 = 48112464
|
|
Ave neighs/atom = 375.879
|
|
Ave special neighs/atom = 7.43187
|
|
Neighbor list builds = 11
|
|
Dangerous builds = 0
|