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lammps/examples/peptide/log.peptide.15Jan10.linux.1
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LAMMPS (15 Jan 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 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
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 = 1.7345 (sec) ----------------
TotEng = -5249.2113 KinEng = 1131.3050 Temp = 281.2023
PotEng = -6380.5163 E_bond = 12.2067 E_angle = 31.7209
E_dihed = 18.8100 E_impro = 2.3598 E_vdwl = 658.0491
E_coul = 26803.5868 E_long = -33907.2495 Press = -1336.8353
SHAKE stats (type/ave/delta) on step 100
4 1.111 1.6521e-06
6 0.996999 2.31654e-06
8 1.08 1.51568e-06
10 1.111 1.39174e-06
12 1.08 5.85504e-07
14 0.959999 0
18 0.9572 8.29238e-06
31 104.52 0.000702966
---------------- Step 100 ----- CPU = 3.4747 (sec) ----------------
TotEng = -5275.3150 KinEng = 1068.4676 Temp = 265.5832
PotEng = -6343.7827 E_bond = 14.4065 E_angle = 43.2073
E_dihed = 15.2137 E_impro = 2.2954 E_vdwl = 707.1690
E_coul = 26780.1086 E_long = -33906.1832 Press = -704.0727
---------------- Step 150 ----- CPU = 5.2211 (sec) ----------------
TotEng = -5332.6748 KinEng = 1078.3846 Temp = 268.0482
PotEng = -6411.0594 E_bond = 17.2300 E_angle = 32.3882
E_dihed = 15.0210 E_impro = 1.6123 E_vdwl = 736.4936
E_coul = 26693.5175 E_long = -33907.3219 Press = -461.0897
SHAKE stats (type/ave/delta) on step 200
4 1.111 1.19442e-06
6 0.997 7.69718e-07
8 1.08 3.18383e-07
10 1.111 1.47546e-06
12 1.08 1.05056e-06
14 0.960001 0
18 0.957201 4.3433e-06
31 104.52 0.000679358
---------------- Step 200 ----- CPU = 6.9746 (sec) ----------------
TotEng = -5338.7112 KinEng = 1098.7385 Temp = 273.1074
PotEng = -6437.4497 E_bond = 18.0357 E_angle = 33.0096
E_dihed = 16.7143 E_impro = 2.6629 E_vdwl = 691.5096
E_coul = 26702.8332 E_long = -33902.2150 Press = -1518.9566
---------------- Step 250 ----- CPU = 8.7706 (sec) ----------------
TotEng = -5291.1132 KinEng = 1066.9455 Temp = 265.2048
PotEng = -6358.0587 E_bond = 14.4150 E_angle = 39.3027
E_dihed = 19.4558 E_impro = 3.0260 E_vdwl = 768.9177
E_coul = 26703.6582 E_long = -33906.8341 Press = -21.1619
SHAKE stats (type/ave/delta) on step 300
4 1.111 6.90984e-07
6 0.997 6.61302e-07
8 1.08 4.62408e-07
10 1.111 1.90648e-06
12 1.08 4.71031e-07
14 0.96 0
18 0.957201 3.69234e-06
31 104.52 0.000432059
---------------- Step 300 ----- CPU = 10.5303 (sec) ----------------
TotEng = -5255.1924 KinEng = 1134.9270 Temp = 282.1026
PotEng = -6390.1194 E_bond = 14.5268 E_angle = 38.2726
E_dihed = 19.1048 E_impro = 2.1050 E_vdwl = 704.1290
E_coul = 26739.7823 E_long = -33908.0399 Press = -687.6630
Loop time of 10.5303 on 1 procs for 300 steps with 2004 atoms
Pair time (%) = 8.07114 (76.6468)
Bond time (%) = 0.0338049 (0.321025)
Kspce time (%) = 1.23794 (11.756)
Neigh time (%) = 0.980866 (9.3147)
Comm time (%) = 0.0597322 (0.567241)
Outpt time (%) = 0.00940299 (0.0892946)
Other time (%) = 0.137415 (1.30495)
FFT time (% of Kspce) = 0.137229 (11.0852)
FFT Gflps 3d (1d only) = 1.19883 1.84775
Nlocal: 2004 ave 2004 max 2004 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11127 ave 11127 max 11127 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 707971 ave 707971 max 707971 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 707971
Ave neighs/atom = 353.279
Ave special neighs/atom = 2.34032
Neighbor list builds = 25
Dangerous builds = 0
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