Homec4science
Diffusion lammps (master) Browse

lammps/examples/peptide/log.peptide.7Jul09.linux.1
8626f1cee6b6master

Last Change
Raw File

log.peptide.7Jul09.linux.1
View Options

LAMMPS (7 Jul 2009)
# Solvated 5-mer peptide
units real
atom_style full
pair_style lj/charmm/coul/long 8.0 10.0 10.0
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
kspace_style pppm 0.0001
read_data data.peptide
3 = max bonds/atom
6 = max angles/atom
14 = max dihedrals/atom
1 = max impropers/atom
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
1 by 1 by 1 processor grid
2004 atoms
2004 velocities
1365 bonds
786 angles
207 dihedrals
12 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
14 = max # of 1-4 neighbors
18 = max # of special neighbors
neighbor 2.0 bin
neigh_modify delay 5
timestep 2.0
thermo_style multi
thermo 50
fix 1 all nvt 275.0 275.0 100.0
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
19 = # of size 2 clusters
6 = # of size 3 clusters
3 = # of size 4 clusters
640 = # of frozen angles
group peptide type <= 12
84 atoms in group peptide
dump 1 peptide atom 10 dump.peptide
dump 2 peptide bond 300 dump.bond
run 300
PPPM initialization ...
G vector = 0.268721
grid = 15 15 15
stencil order = 5
RMS precision = 4.86052e-05
brick FFT buffer size/proc = 10648 3375 5808
SHAKE stats (type/ave/delta) on step 0
4 1.111 1.44264e-05
6 0.996998 7.26967e-06
8 1.08 1.32536e-05
10 1.111 1.22749e-05
12 1.08 1.11767e-05
14 0.96 0
18 0.957206 4.37979e-05
31 104.519 0.00396029
Memory usage per processor = 19.2806 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26771.8055 E_long = -33907.4679 Press = -845.4767
---------------- Step 50 ----- CPU = 1.9084 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9512 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1773
E_coul = 26803.9885 E_long = -33907.2410 Press = -1331.7941
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80751e-07
6 0.997 1.06201e-06
8 1.08 6.20437e-07
10 1.111 6.23402e-07
12 1.08 2.68046e-07
14 0.96 0
18 0.957201 5.38003e-06
31 104.52 0.000502302
---------------- Step 100 ----- CPU = 3.8132 (sec) ----------------
TotEng = -5257.9998 KinEng = 1078.0523 Temp = 267.9656
PotEng = -6336.0521 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3270
E_coul = 26786.2252 E_long = -33906.1028 Press = -648.6625
---------------- Step 150 ----- CPU = 5.7645 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6038 Temp = 273.0740
PotEng = -6385.8884 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9699
E_coul = 26716.7972 E_long = -33906.8217 Press = -333.1793
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50912e-07
8 1.08 6.58565e-08
10 1.111 5.56675e-07
12 1.08 1.99343e-07
14 0.96 0
18 0.957201 3.59691e-06
31 104.52 0.000388135
---------------- Step 200 ----- CPU = 7.6254 (sec) ----------------
TotEng = -5308.4506 KinEng = 1100.5139 Temp = 273.5487
PotEng = -6408.9645 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3197
E_coul = 26735.6532 E_long = -33901.9330 Press = -1470.4759
---------------- Step 250 ----- CPU = 9.5790 (sec) ----------------
TotEng = -5294.1810 KinEng = 1071.1657 Temp = 266.2538
PotEng = -6365.3468 E_bond = 14.2024 E_angle = 39.1969
E_dihed = 19.4546 E_impro = 3.1388 E_vdwl = 753.6297
E_coul = 26713.2917 E_long = -33908.2610 Press = -187.7503
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78101e-06
6 0.997001 3.5121e-06
8 1.08 2.09172e-06
10 1.111 5.64083e-06
12 1.08 2.10195e-06
14 0.96 0
18 0.957202 7.62681e-06
31 104.52 0.000805945
---------------- Step 300 ----- CPU = 11.5293 (sec) ----------------
TotEng = -5251.4412 KinEng = 1123.4657 Temp = 279.2537
PotEng = -6374.9069 E_bond = 14.2235 E_angle = 38.4664
E_dihed = 18.1383 E_impro = 2.3705 E_vdwl = 715.5989
E_coul = 26744.9563 E_long = -33908.6606 Press = -467.2646
Loop time of 11.5293 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 8.87232 (76.9545)
Bond time (%) = 0.0325627 (0.282434)
Kspce time (%) = 1.23912 (10.7476)
Neigh time (%) = 1.18853 (10.3088)
Comm time (%) = 0.0631688 (0.547897)
Outpt time (%) = 0.00623298 (0.054062)
Other time (%) = 0.127376 (1.1048)
FFT time (% of Kspce) = 0.137515 (11.0978)
FFT Gflps 3d (1d only) = 1.19633 1.84006
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11181 ave 11181 max 11181 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 708030 ave 708030 max 708030 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708030
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
c4science · Help