Homec4science
Diffusion lammps (master) Browse

lammps/examples/peptide/log.peptide.22Jun07.liberty.4
f95ccaf03551master

Last Change
Raw File

log.peptide.22Jun07.liberty.4
View Options

LAMMPS (22 June 2007)
# 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 2 by 2 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 = 0.268725
grid = 15 15 15
RMS precision = 4.85953e-05
brick FFT buffer size/proc = 4312 960 3696
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 = 8.97394 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4579 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 = 26772.2794 E_long = -33907.9417 Press = -845.4771
---------------- Step 50 ----- CPU = 1.0767 (sec) ----------------
TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774
E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80748e-07
6 0.997 1.06201e-06
8 1.08 6.20434e-07
10 1.111 6.23399e-07
12 1.08 2.68045e-07
14 0.96 0
18 0.957201 5.38002e-06
31 104.52 0.000502303
---------------- Step 100 ----- CPU = 2.1741 (sec) ----------------
TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656
PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271
E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634
---------------- Step 150 ----- CPU = 3.3006 (sec) ----------------
TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698
E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18831e-07
6 0.997 1.50909e-07
8 1.08 6.58563e-08
10 1.111 5.56695e-07
12 1.08 1.99338e-07
14 0.96 0
18 0.957201 3.59689e-06
31 104.52 0.000388134
---------------- Step 200 ----- CPU = 4.4047 (sec) ----------------
TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480
PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209
E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571
---------------- Step 250 ----- CPU = 5.5320 (sec) ----------------
TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530
PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972
E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340
E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78173e-06
6 0.997001 3.51761e-06
8 1.08 2.09202e-06
10 1.111 5.64179e-06
12 1.08 2.10252e-06
14 0.96 0
18 0.957202 7.62675e-06
31 104.52 0.00080599
---------------- Step 300 ----- CPU = 6.6418 (sec) ----------------
TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484
PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644
E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075
E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013
Loop time of 6.64219 on 4 procs for 300 steps with 2004 atoms
Pair time (%) = 3.83138 (57.6825)
Bond time (%) = 0.0190526 (0.286843)
Kspce time (%) = 1.23672 (18.6191)
Neigh time (%) = 0.383302 (5.77072)
Comm time (%) = 0.699462 (10.5306)
Outpt time (%) = 0.0126947 (0.191122)
Other time (%) = 0.459581 (6.91913)
FFT time (% of Kspce) = 0.217534 (17.5896)
FFT Gflps 3d 1d-only = 0.756267 3.92102
Nlocal: 501 ave 508 max 490 min
Histogram: 1 0 0 0 0 0 1 1 0 1
Nghost: 6586.25 ave 6628 max 6548 min
Histogram: 1 0 1 0 0 0 1 0 0 1
Neighs: 177008 ave 180559 max 170208 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 708030
Ave neighs/atom = 353.308
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
c4science · Help