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lammps/examples/peptide/log.peptide.10Sep10.linux.1
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LAMMPS (10 Sep 2010)
# 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 temp 275.0 275.0 100.0 tchain 1
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
compute bnd all property/local btype batom1 batom2
dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
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 = 19.6255 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 = 26771.8055 E_long = -33907.4679 Press = -845.4762
---------------- Step 50 ----- CPU = 1.7281 (sec) ----------------
TotEng = -5247.5491 KinEng = 1132.4011 Temp = 281.4748
PotEng = -6379.9502 E_bond = 12.2118 E_angle = 31.7365
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1770
E_coul = 26803.9897 E_long = -33907.2410 Press = -1331.7985
SHAKE stats (type/ave/delta) on step 100
4 1.111 7.80799e-07
6 0.997 1.06209e-06
8 1.08 6.20484e-07
10 1.111 6.23444e-07
12 1.08 2.68063e-07
14 0.96 0
18 0.957201 5.38017e-06
31 104.52 0.000502314
---------------- Step 100 ----- CPU = 3.4571 (sec) ----------------
TotEng = -5257.9973 KinEng = 1078.0555 Temp = 267.9664
PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
E_coul = 26786.2248 E_long = -33906.1028 Press = -648.6626
---------------- Step 150 ----- CPU = 5.2286 (sec) ----------------
TotEng = -5287.2845 KinEng = 1098.6039 Temp = 273.0740
PotEng = -6385.8884 E_bond = 17.4924 E_angle = 32.8593
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
E_coul = 26716.7990 E_long = -33906.8220 Press = -333.1912
SHAKE stats (type/ave/delta) on step 200
4 1.111 2.18836e-07
6 0.997 1.50836e-07
8 1.08 6.58288e-08
10 1.111 5.55388e-07
12 1.08 1.99221e-07
14 0.96 0
18 0.957201 3.59665e-06
31 104.52 0.000388185
---------------- Step 200 ----- CPU = 6.9347 (sec) ----------------
TotEng = -5308.4531 KinEng = 1100.5081 Temp = 273.5473
PotEng = -6408.9612 E_bond = 18.2714 E_angle = 33.3035
E_dihed = 16.8150 E_impro = 2.6054 E_vdwl = 686.3253
E_coul = 26735.6523 E_long = -33901.9341 Press = -1470.4125
---------------- Step 250 ----- CPU = 8.7214 (sec) ----------------
TotEng = -5294.1792 KinEng = 1071.1639 Temp = 266.2534
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1951
E_dihed = 19.4554 E_impro = 3.1386 E_vdwl = 753.5442
E_coul = 26713.3849 E_long = -33908.2636 Press = -188.7523
SHAKE stats (type/ave/delta) on step 300
4 1.111 3.78179e-06
6 0.997001 3.49519e-06
8 1.08 2.09282e-06
10 1.111 5.64213e-06
12 1.08 2.10337e-06
14 0.96 0
18 0.957202 7.67605e-06
31 104.52 0.000806296
---------------- Step 300 ----- CPU = 10.5074 (sec) ----------------
TotEng = -5251.4367 KinEng = 1123.6271 Temp = 279.2938
PotEng = -6375.0637 E_bond = 14.2250 E_angle = 38.4733
E_dihed = 18.1306 E_impro = 2.3699 E_vdwl = 715.4580
E_coul = 26744.9478 E_long = -33908.6682 Press = -469.4705
Loop time of 10.5074 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 8.09483 (77.0391)
Bond time (%) = 0.0333912 (0.317787)
Kspce time (%) = 1.22243 (11.6339)
Neigh time (%) = 0.947993 (9.02212)
Comm time (%) = 0.0614872 (0.585178)
Outpt time (%) = 0.00946116 (0.0900426)
Other time (%) = 0.137843 (1.31186)
FFT time (% of Kspce) = 0.137887 (11.2798)
FFT Gflps 3d (1d only) = 1.19311 1.83273
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: 708037 ave 708037 max 708037 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 708037
Ave neighs/atom = 353.312
Ave special neighs/atom = 2.34032
Neighbor list builds = 26
Dangerous builds = 0
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