forked from lijiext/lammps
136 lines
4.1 KiB
Groff
136 lines
4.1 KiB
Groff
|
LAMMPS (1 Feb 2014)
|
||
|
|
# Rhodopsin model
|
||
|
|
|
||
|
|
newton off
|
||
|
|
package gpu force/neigh 0 1 1
|
||
|
|
|
||
|
|
variable x index 2
|
||
|
|
variable y index 2
|
||
|
|
variable z index 2
|
||
|
|
|
||
|
|
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/gpu 8.0 10.0
|
||
|
|
pair_modify mix arithmetic
|
||
|
|
kspace_style pppm/gpu 1e-4
|
||
|
|
|
||
|
|
read_data data.rhodo
|
||
|
|
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||
|
|
1 by 2 by 2 MPI processor grid
|
||
|
|
reading atoms ...
|
||
|
|
32000 atoms
|
||
|
|
reading velocities ...
|
||
|
|
32000 velocities
|
||
|
|
scanning bonds ...
|
||
|
|
4 = max bonds/atom
|
||
|
|
scanning angles ...
|
||
|
|
18 = max angles/atom
|
||
|
|
scanning dihedrals ...
|
||
|
|
40 = max dihedrals/atom
|
||
|
|
scanning impropers ...
|
||
|
|
4 = 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 2
|
||
|
|
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||
|
|
1 by 2 by 2 MPI processor grid
|
||
|
|
256000 atoms
|
||
|
|
221784 bonds
|
||
|
|
323736 angles
|
||
|
|
454632 dihedrals
|
||
|
|
8272 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
|
||
|
|
12936 = # of size 2 clusters
|
||
|
|
29064 = # of size 3 clusters
|
||
|
|
5976 = # of size 4 clusters
|
||
|
|
33864 = # 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 100
|
||
|
|
thermo_style multi
|
||
|
|
timestep 2.0
|
||
|
|
|
||
|
|
run 200
|
||
|
|
PPPM initialization ...
|
||
|
|
G vector (1/distance) = 0.245959
|
||
|
|
grid = 48 64 60
|
||
|
|
stencil order = 5
|
||
|
|
estimated absolute RMS force accuracy = 0.0410392
|
||
|
|
estimated relative force accuracy = 0.000123588
|
||
|
|
using double precision FFTs
|
||
|
|
3d grid and FFT values/proc = 68635 46080
|
||
|
|
Memory usage per processor = 250.358 Mbytes
|
||
|
|
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||
|
|
TotEng = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
|
||
|
|
PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
|
||
|
|
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
|
||
|
|
E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
|
||
|
|
Volume = 2457390.7959
|
||
|
|
---------------- Step 100 ----- CPU = 12.3409 (sec) ----------------
|
||
|
|
TotEng = -233301.6797 KinEng = 123222.9259 Temp = 214.7790
|
||
|
|
PotEng = -356524.6057 E_bond = 13098.4672 E_angle = 56766.9111
|
||
|
|
E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
|
||
|
|
E_coul = 1705084.7688 E_long = -2137481.5867 Press = -1634.3910
|
||
|
|
Volume = 2522232.6302
|
||
|
|
---------------- Step 200 ----- CPU = 23.6590 (sec) ----------------
|
||
|
|
TotEng = -308341.9699 KinEng = 108937.4196 Temp = 189.8792
|
||
|
|
PotEng = -417279.3895 E_bond = 9579.0134 E_angle = 47373.6274
|
||
|
|
E_dihed = 39847.4807 E_impro = 967.6755 E_vdwl = -23635.2996
|
||
|
|
E_coul = 1646633.5046 E_long = -2138045.3916 Press = -1185.9299
|
||
|
|
Volume = 2554683.1519
|
||
|
|
Loop time of 23.6591 on 4 procs for 200 steps with 256000 atoms
|
||
|
|
|
||
|
|
Pair time (%) = 4.81669 (20.3587)
|
||
|
|
Bond time (%) = 6.52579 (27.5826)
|
||
|
|
Kspce time (%) = 4.48765 (18.968)
|
||
|
|
Neigh time (%) = 1.3238 (5.5953)
|
||
|
|
Comm time (%) = 0.490551 (2.07342)
|
||
|
|
Outpt time (%) = 0.000454485 (0.00192098)
|
||
|
|
Other time (%) = 6.01414 (25.42)
|
||
|
|
|
||
|
|
FFT time (% of Kspce) = 1.77734 (39.6051)
|
||
|
|
FFT Gflps 3d (1d only) = 5.02949 11.6654
|
||
|
|
|
||
|
|
Nlocal: 64000 ave 64001 max 63999 min
|
||
|
|
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||
|
|
Nghost: 70656.5 ave 70660 max 70654 min
|
||
|
|
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||
|
|
Neighs: 0 ave 0 max 0 min
|
||
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||
|
|
|
||
|
|
Total # of neighbors = 0
|
||
|
|
Ave neighs/atom = 0
|
||
|
|
Ave special neighs/atom = 7.43187
|
||
|
|
Neighbor list builds = 31
|
||
|
|
Dangerous builds = 12
|
||
|
|
|
||
|
|
Please see the log.cite file for references relevant to this simulation
|
||
|
|
|