Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/examples/peptide/log.peptide.1Oct06.linux.1
f25713e3b02dlammm-devel

Last Change
Raw File

log.peptide.1Oct06.linux.1
View Options

LAMMPS (1 Oct 2006)
# 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
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 = 0.268725
grid = 15 15 15
RMS precision = 4.85953e-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 = 19.9477 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4557 KinEng = 1134.9184 Temp = 282.1027
PotEng = -6372.3741 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2705 E_long = -33907.9305 Press = -845.7315
---------------- Step 50 ----- CPU = 7.8391 (sec) ----------------
TotEng = -5247.5537 KinEng = 1132.3981 Temp = 281.4762
PotEng = -6379.9518 E_bond = 12.2118 E_angle = 31.7364
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1762
E_coul = 26804.4518 E_long = -33907.7036 Press = -1332.2322
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.81219e-07
6 0.997 1.06269e-06
8 1.08 6.20924e-07
10 1.111 6.23819e-07
12 1.08 2.68216e-07
14 0.96 0
18 0.957201 5.38162e-06
31 104.52 0.000502412
---------------- Step 100 ----- CPU = 15.6343 (sec) ----------------
TotEng = -5258.0208 KinEng = 1078.0404 Temp = 267.9647
PotEng = -6336.0612 E_bond = 14.4827 E_angle = 43.4425
E_dihed = 15.2568 E_impro = 2.3160 E_vdwl = 708.3258
E_coul = 26786.6805 E_long = -33906.5655 Press = -648.9282
---------------- Step 150 ----- CPU = 23.5108 (sec) ----------------
TotEng = -5287.3158 KinEng = 1098.5907 Temp = 273.0729
PotEng = -6385.9065 E_bond = 17.4922 E_angle = 32.8590
E_dihed = 15.1622 E_impro = 1.6521 E_vdwl = 736.9709
E_coul = 26717.2418 E_long = -33907.2848 Press = -333.3566
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18765e-07
6 0.997 1.50571e-07
8 1.08 6.57567e-08
10 1.111 5.57115e-07
12 1.08 1.98908e-07
14 0.96 0
18 0.957201 3.59647e-06
31 104.52 0.000388049
---------------- Step 200 ----- CPU = 31.1103 (sec) ----------------
TotEng = -5308.4800 KinEng = 1100.4956 Temp = 273.5463
PotEng = -6408.9756 E_bond = 18.2711 E_angle = 33.3032
E_dihed = 16.8153 E_impro = 2.6053 E_vdwl = 686.3176
E_coul = 26736.1059 E_long = -33902.3940 Press = -1470.9775
---------------- Step 250 ----- CPU = 39.2012 (sec) ----------------
TotEng = -5294.1836 KinEng = 1071.1372 Temp = 266.2488
PotEng = -6365.3209 E_bond = 14.2026 E_angle = 39.1962
E_dihed = 19.4540 E_impro = 3.1384 E_vdwl = 753.6645
E_coul = 26713.7437 E_long = -33908.7203 Press = -187.3211
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78222e-06
6 0.997001 3.50327e-06
8 1.08 2.09306e-06
10 1.111 5.643e-06
12 1.08 2.10265e-06
14 0.96 0
18 0.957202 7.61122e-06
31 104.52 0.000804522
---------------- Step 300 ----- CPU = 47.1755 (sec) ----------------
TotEng = -5251.4247 KinEng = 1123.3204 Temp = 279.2198
PotEng = -6374.7450 E_bond = 14.2228 E_angle = 38.4702
E_dihed = 18.1329 E_impro = 2.3701 E_vdwl = 715.7685
E_coul = 26745.4242 E_long = -33909.1337 Press = -464.7492
Loop time of 47.1756 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 38.5968 (81.8151)
Bond time (%) = 0.077238 (0.163724)
Kspce time (%) = 3.51546 (7.45187)
Neigh time (%) = 4.11099 (8.71422)
Comm time (%) = 0.360056 (0.763225)
Outpt time (%) = 0.017432 (0.0369513)
Other time (%) = 0.497656 (1.0549)
FFT time (% of Kspce) = 1.1808 (33.5887)
FFT Gflps 3d 1d-only = 0.139324 0.209866
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: 708038 ave 708038 max 708038 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708038
Ave neighs/atom = 353.312
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
c4science · Help