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lammps/bench/POTENTIALS/log.26Jun12.protein.1
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LAMMPS (29 Jun 2012)
# Rhodopsin model
units real
neighbor 2.0 bin
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.protein
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 1 by 1 MPI 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
special_bonds charmm
thermo_style multi
timestep 2.0
run 100
PPPM initialization ...
G vector (1/distance) = 0.248831
grid = 25 32 32
stencil order = 5
estimated absolute RMS force accuracy = 0.025142
estimated relative force accuracy = 7.57143e-05
using double precision FFTs
brick FFT buffer size/proc = 41070 25600 12321
Memory usage per processor = 139.274 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
Volume = 307995.0335
---------------- Step 100 ----- CPU = 36.1778 (sec) ----------------
TotEng = -25290.7641 KinEng = 21592.0080 Temp = 301.0920
PotEng = -46882.7721 E_bond = 2567.9806 E_angle = 10781.9408
E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804
E_coul = 206654.9996 E_long = -270400.7390 Press = 6.9875
Volume = 308133.9900
Loop time of 36.1779 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 25.7884 (71.2822)
Bond time (%) = 1.2794 (3.53643)
Kspce time (%) = 3.29168 (9.0986)
Neigh time (%) = 4.43537 (12.2599)
Comm time (%) = 0.0717564 (0.198343)
Outpt time (%) = 0.000114918 (0.000317646)
Other time (%) = 1.31117 (3.62423)
FFT time (% of Kspce) = 0.27822 (8.45222)
FFT Gflps 3d (1d only) = 1.86794 3.25864
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 47958 ave 47958 max 47958 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12028107
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11
Dangerous builds = 0
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