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lammps/examples/peptide/log.peptide.5Oct07.linux.1
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LAMMPS (5 Oct 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 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 = 19.8528 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
E_coul = 26772.2793 E_long = -33907.9417 Press = -845.4779
---------------- Step 50 ----- CPU = 1.9606 (sec) ----------------
TotEng = -5247.5483 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 = 658.1774
E_coul = 26804.4623 E_long = -33907.7148 Press = -1331.7938
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80749e-07
6 0.997 1.06201e-06
8 1.08 6.20434e-07
10 1.111 6.234e-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 = 3.9195 (sec) ----------------
TotEng = -5257.9999 KinEng = 1078.0523 Temp = 267.9656
PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3270
E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6633
---------------- Step 150 ----- CPU = 5.9212 (sec) ----------------
TotEng = -5287.2846 KinEng = 1098.6036 Temp = 273.0739
PotEng = -6385.8882 E_bond = 17.4924 E_angle = 32.8594
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9697
E_coul = 26717.2713 E_long = -33907.2954 Press = -333.1850
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18838e-07
6 0.997 1.50926e-07
8 1.08 6.58607e-08
10 1.111 5.5663e-07
12 1.08 1.99359e-07
14 0.96 0
18 0.957201 3.5969e-06
31 104.52 0.000388142
---------------- Step 200 ----- CPU = 7.8333 (sec) ----------------
TotEng = -5308.4510 KinEng = 1100.5111 Temp = 273.5480
PotEng = -6408.9621 E_bond = 18.2713 E_angle = 33.3035
E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3210
E_coul = 26736.1280 E_long = -33902.4065 Press = -1470.4562
---------------- Step 250 ----- CPU = 9.8434 (sec) ----------------
TotEng = -5294.1869 KinEng = 1071.1638 Temp = 266.2533
PotEng = -6365.3507 E_bond = 14.2025 E_angle = 39.1971
E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6323
E_coul = 26713.7588 E_long = -33908.7351 Press = -187.8267
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78194e-06
6 0.997001 3.51756e-06
8 1.08 2.09218e-06
10 1.111 5.64208e-06
12 1.08 2.10271e-06
14 0.96 0
18 0.957202 7.6303e-06
31 104.52 0.000806088
---------------- Step 300 ----- CPU = 11.8512 (sec) ----------------
TotEng = -5251.4345 KinEng = 1123.4544 Temp = 279.2509
PotEng = -6374.8890 E_bond = 14.2234 E_angle = 38.4645
E_dihed = 18.1397 E_impro = 2.3705 E_vdwl = 715.5940
E_coul = 26745.4502 E_long = -33909.1312 Press = -467.2462
Loop time of 11.8512 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 9.17722 (77.4371)
Bond time (%) = 0.032975 (0.278241)
Kspce time (%) = 1.24933 (10.5418)
Neigh time (%) = 1.19696 (10.0999)
Comm time (%) = 0.0635979 (0.536637)
Outpt time (%) = 0.00585294 (0.0493869)
Other time (%) = 0.125263 (1.05696)
FFT time (% of Kspce) = 0.137701 (11.022)
FFT Gflps 3d 1d-only = 1.19472 1.73748
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: 708035 ave 708035 max 708035 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708035
Ave neighs/atom = 353.311
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
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