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lammps/bench/log.1Oct06.rhodo.lmp.fixed.linux.1
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log.1Oct06.rhodo.lmp.fixed.linux.1
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LAMMPS (1 Oct 2006)
# 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
4 = max bonds/atom
8 = max angles/atom
18 = max dihedrals/atom
2 = max impropers/atom
1 by 1 by 1 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
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 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 = 0.245875
grid = 24 32 30
RMS precision = 8.76365e-05
brick FFT buffer size/proc = 37555 23040 11655
Memory usage per processor = 134.397 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25355.8070 KinEng = 21444.8287 Temp = 299.0420
PotEng = -46800.6357 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 203819.9996 E_long = -267197.4382 Press = -142.0854
Volume = 307995.0335
---------------- Step 50 ----- CPU = 158.6744 (sec) ----------------
TotEng = -25330.0515 KinEng = 21500.8719 Temp = 299.8235
PotEng = -46830.9234 E_bond = 2471.7510 E_angle = 10836.5171
E_dihed = 5239.6981 E_impro = 227.1295 E_vdwl = -1992.9813
E_coul = 203591.2432 E_long = -267204.2808 Press = 238.5401
Volume = 308031.8248
---------------- Step 100 ----- CPU = 322.3292 (sec) ----------------
TotEng = -25291.9828 KinEng = 21589.3087 Temp = 301.0567
PotEng = -46881.2915 E_bond = 2568.0314 E_angle = 10781.6607
E_dihed = 5198.3574 E_impro = 216.6809 E_vdwl = -1898.4756
E_coul = 203451.1288 E_long = -267198.6749 Press = 10.7061
Volume = 308134.7569
Loop time of 322.329 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 239.178 (74.203)
Bond time (%) = 7.33387 (2.27527)
Kspce time (%) = 19.0626 (5.914)
Neigh time (%) = 49.7111 (15.4224)
Comm time (%) = 0.930179 (0.28858)
Outpt time (%) = 0.003927 (0.00121832)
Other time (%) = 6.10957 (1.89544)
FFT time (% of Kspce) = 4.06694 (21.3347)
FFT Gflps 3d 1d-only = 0.113814 0.261395
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47962 ave 47962 max 47962 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.2028e+07 ave 1.2028e+07 max 1.2028e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12027974
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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