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lammps/bench/log.22Jun07.rhodo.fixed.liberty.8
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log.22Jun07.rhodo.fixed.liberty.8
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LAMMPS (22 June 2007)
# 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
orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615)
2 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
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 = 7140 3072 3780
Memory usage per processor = 30.031 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25355.8254 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46800.6567 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 203820.0671 E_long = -267197.5267 Press = -142.0456
Volume = 307995.0335
---------------- Step 50 ----- CPU = 10.1023 (sec) ----------------
TotEng = -25329.9175 KinEng = 21500.9583 Temp = 299.8223
PotEng = -46830.8758 E_bond = 2471.7583 E_angle = 10836.5458
E_dihed = 5239.7029 E_impro = 227.1302 E_vdwl = -1992.9669
E_coul = 203591.3230 E_long = -267204.3691 Press = 238.4815
Volume = 308031.8243
---------------- Step 100 ----- CPU = 20.8372 (sec) ----------------
TotEng = -25291.5484 KinEng = 21589.5399 Temp = 301.0576
PotEng = -46881.0883 E_bond = 2568.0537 E_angle = 10781.7480
E_dihed = 5198.3744 E_impro = 216.6829 E_vdwl = -1898.4511
E_coul = 203451.2661 E_long = -267198.7623 Press = 10.7451
Volume = 308134.7692
Loop time of 20.8381 on 8 procs for 100 steps with 32000 atoms
Pair time (%) = 13.4637 (64.6111)
Bond time (%) = 0.525574 (2.52218)
Kspce time (%) = 3.3461 (16.0576)
Neigh time (%) = 1.63546 (7.84842)
Comm time (%) = 0.770115 (3.69571)
Outpt time (%) = 0.00124443 (0.00597188)
Other time (%) = 1.09588 (5.25903)
FFT time (% of Kspce) = 0.715048 (21.3696)
FFT Gflps 3d 1d-only = 0.647331 7.04904
Nlocal: 4000 ave 4083 max 3940 min
Histogram: 2 1 0 1 2 0 0 0 1 1
Nghost: 16028.4 ave 16084 max 15941 min
Histogram: 1 0 0 2 0 1 0 0 2 2
Neighs: 1.5035e+06 ave 1.55024e+06 max 1.46322e+06 min
Histogram: 2 0 1 0 2 1 0 0 0 2
Total # of neighbors = 12027978
Ave neighs/atom = 375.874
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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