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lammps/bench/log.21May08.rhodo.fixed.linux.4
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LAMMPS (21 May 2008)
# 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)
1 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 = 0.248831
grid = 25 32 32
RMS precision = 7.57143e-05
brick FFT buffer size/proc = 13230 6400 5670
Memory usage per processor = 47.7552 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2081 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0393 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6578 E_long = -270399.5000 Press = -142.6055
Volume = 307995.0335
---------------- Step 50 ----- CPU = 9.3719 (sec) ----------------
TotEng = -25330.0565 KinEng = 21501.0002 Temp = 299.8229
PotEng = -46831.0567 E_bond = 2471.7010 E_angle = 10836.4978
E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2861
E_coul = 206793.4380 E_long = -270406.1593 Press = 237.6633
Volume = 308031.6776
---------------- Step 100 ----- CPU = 19.0243 (sec) ----------------
TotEng = -25290.7382 KinEng = 21592.0112 Temp = 301.0920
PotEng = -46882.7494 E_bond = 2567.9820 E_angle = 10781.9426
E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4962
E_coul = 206655.0352 E_long = -270400.7391 Press = 6.9485
Volume = 308134.2307
Loop time of 19.025 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 12.4734 (65.5633)
Bond time (%) = 0.675595 (3.55109)
Kspce time (%) = 2.50745 (13.1798)
Neigh time (%) = 1.92768 (10.1324)
Comm time (%) = 0.513097 (2.69697)
Outpt time (%) = 0.00170368 (0.00895496)
Other time (%) = 0.92605 (4.86755)
FFT time (% of Kspce) = 0.410454 (16.3694)
FFT Gflps 3d 1d-only = 1.26615 6.83721
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
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96493e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12028097
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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