forked from lijiext/lammps
132 lines
4.1 KiB
Groff
132 lines
4.1 KiB
Groff
LAMMPS (30 Apr 2015)
|
|
# 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
|
|
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
|
|
1 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
32000 atoms
|
|
reading velocities ...
|
|
32000 velocities
|
|
scanning bonds ...
|
|
4 = max bonds/atom
|
|
scanning angles ...
|
|
8 = max angles/atom
|
|
scanning dihedrals ...
|
|
18 = max dihedrals/atom
|
|
scanning impropers ...
|
|
2 = max impropers/atom
|
|
reading bonds ...
|
|
27723 bonds
|
|
reading angles ...
|
|
40467 angles
|
|
reading dihedrals ...
|
|
56829 dihedrals
|
|
reading impropers ...
|
|
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 MPI 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 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) = 0.248593
|
|
grid = 48 60 36
|
|
stencil order = 5
|
|
estimated absolute RMS force accuracy = 0.0359793
|
|
estimated relative force accuracy = 0.00010835
|
|
using double precision FFTs
|
|
3d grid and FFT values/proc = 41615 25920
|
|
Neighbor list info ...
|
|
1 neighbor list requests
|
|
update every 1 steps, delay 5 steps, check yes
|
|
master list distance cutoff = 12
|
|
Memory usage per processor = 95.5339 Mbytes
|
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
|
TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304
|
|
PotEng = -187204.8138 E_bond = 10151.9760 E_angle = 43685.4968
|
|
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
|
|
E_coul = 827053.5824 E_long = -1080565.6077 Press = -142.3092
|
|
Volume = 1231980.1340
|
|
---------------- Step 50 ----- CPU = 18.5923 (sec) ----------------
|
|
TotEng = -101320.2677 KinEng = 86003.4837 Temp = 299.8118
|
|
PotEng = -187323.7514 E_bond = 9887.1072 E_angle = 43346.7922
|
|
E_dihed = 20958.7032 E_impro = 908.4715 E_vdwl = -7973.4457
|
|
E_coul = 826141.3831 E_long = -1080592.7629 Press = 238.0161
|
|
Volume = 1232126.1855
|
|
---------------- Step 100 ----- CPU = 38.1551 (sec) ----------------
|
|
TotEng = -101158.1849 KinEng = 86355.6149 Temp = 301.0393
|
|
PotEng = -187513.7998 E_bond = 10272.0693 E_angle = 43128.6454
|
|
E_dihed = 20793.9759 E_impro = 867.0826 E_vdwl = -7586.7186
|
|
E_coul = 825583.7122 E_long = -1080572.5667 Press = 15.2151
|
|
Volume = 1232535.8423
|
|
Loop time of 38.1551 on 4 procs for 100 steps with 128000 atoms
|
|
|
|
Pair time (%) = 26.4472 (69.3149)
|
|
Bond time (%) = 1.31402 (3.44388)
|
|
Kspce time (%) = 4.23553 (11.1008)
|
|
Neigh time (%) = 4.45503 (11.6761)
|
|
Comm time (%) = 0.208946 (0.547622)
|
|
Outpt time (%) = 0.000290096 (0.000760307)
|
|
Other time (%) = 1.49411 (3.91587)
|
|
|
|
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 = 48112472
|
|
Ave neighs/atom = 375.879
|
|
Ave special neighs/atom = 7.43187
|
|
Neighbor list builds = 11
|
|
Dangerous builds = 0
|