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Steve Plimpton
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LAMMPS (6 Oct 2016)
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# 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
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
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 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 ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
G vector (1/distance) = 0.248835
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.0355478
estimated relative force accuracy = 0.000107051
using double precision FFTs
3d grid and FFT values/proc = 13230 6400
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 5 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6 -> bins = 10 13 13
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Memory usage per processor = 37.3604 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
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E_coul = 207025.8927 E_long = -270403.7333 Press = -149.3301
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---------------- Step 50 ----- CPU = 4.6056 (sec) ----------------
TotEng = -25330.0321 KinEng = 21501.0036 Temp = 299.8230
PotEng = -46831.0357 E_bond = 2471.7033 E_angle = 10836.5108
E_dihed = 5239.6316 E_impro = 227.1219 E_vdwl = -1993.2763
E_coul = 206797.6655 E_long = -270410.3927 Press = 237.6866
Volume = 308031.5640
---------------- Step 100 ----- CPU = 9.3910 (sec) ----------------
TotEng = -25290.7386 KinEng = 21591.9096 Temp = 301.0906
PotEng = -46882.6482 E_bond = 2567.9789 E_angle = 10781.9556
E_dihed = 5198.7493 E_impro = 216.7863 E_vdwl = -1902.6458
E_coul = 206659.5007 E_long = -270404.9733 Press = 6.7898
Volume = 308133.9933
Loop time of 9.39107 on 4 procs for 100 steps with 32000 atoms
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Performance: 1.840 ns/day, 13.043 hours/ns, 10.648 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
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Pair | 6.2189 | 6.3266 | 6.6072 | 6.5 | 67.37
Bond | 0.30793 | 0.32122 | 0.3414 | 2.4 | 3.42
Kspace | 0.87994 | 1.1644 | 1.2855 | 15.3 | 12.40
Neigh | 1.1358 | 1.136 | 1.1362 | 0.0 | 12.10
Comm | 0.08292 | 0.084935 | 0.087077 | 0.5 | 0.90
Output | 0.00015712 | 0.00016558 | 0.00018501 | 0.1 | 0.00
Modify | 0.33717 | 0.34246 | 0.34794 | 0.7 | 3.65
Other | | 0.01526 | | | 0.16
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
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Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96492e+06 min
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Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
Steve Plimpton
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Total wall time: 0:00:09