forked from lijiext/lammps
157 lines
5.5 KiB
Groff
157 lines
5.5 KiB
Groff
LAMMPS (9 Jan 2009)
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# Solvated 5-mer peptide
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units real
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atom_style full
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pair_style lj/charmm/coul/long 8.0 10.0 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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kspace_style pppm 0.0001
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read_data data.peptide
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3 = max bonds/atom
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6 = max angles/atom
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14 = max dihedrals/atom
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1 = max impropers/atom
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orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
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1 by 2 by 2 processor grid
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2004 atoms
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2004 velocities
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1365 bonds
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786 angles
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207 dihedrals
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12 impropers
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4 = max # of 1-2 neighbors
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7 = max # of 1-3 neighbors
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14 = max # of 1-4 neighbors
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18 = max # of special neighbors
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neighbor 2.0 bin
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neigh_modify delay 5
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timestep 2.0
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thermo_style multi
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thermo 50
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fix 1 all nvt 275.0 275.0 100.0
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fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
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19 = # of size 2 clusters
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6 = # of size 3 clusters
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3 = # of size 4 clusters
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640 = # of frozen angles
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group peptide type <= 12
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84 atoms in group peptide
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dump 1 peptide atom 10 dump.peptide
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dump 2 peptide bond 300 dump.bond
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run 300
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PPPM initialization ...
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G vector = 0.268721
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grid = 15 15 15
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stencil order = 5
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RMS precision = 4.86052e-05
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brick FFT buffer size/proc = 4312 960 3696
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SHAKE stats (type/ave/delta) on step 0
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4 1.111 1.44264e-05
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6 0.996998 7.26967e-06
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8 1.08 1.32536e-05
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10 1.111 1.22749e-05
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12 1.08 1.11767e-05
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14 0.96 0
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18 0.957206 4.37979e-05
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31 104.519 0.00396029
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Memory usage per processor = 8.58908 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
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PotEng = -6372.3765 E_bond = 16.5572 E_angle = 36.3726
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E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
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E_coul = 26771.8055 E_long = -33907.4679 Press = -845.4767
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---------------- Step 50 ----- CPU = 0.6167 (sec) ----------------
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TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
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PotEng = -6379.9512 E_bond = 12.2118 E_angle = 31.7365
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E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1773
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E_coul = 26803.9885 E_long = -33907.2410 Press = -1331.7941
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 7.80751e-07
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6 0.997 1.06201e-06
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8 1.08 6.20437e-07
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10 1.111 6.23402e-07
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12 1.08 2.68046e-07
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14 0.96 0
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18 0.957201 5.38003e-06
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31 104.52 0.000502302
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---------------- Step 100 ----- CPU = 1.2313 (sec) ----------------
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TotEng = -5257.9998 KinEng = 1078.0523 Temp = 267.9656
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PotEng = -6336.0521 E_bond = 14.4828 E_angle = 43.4429
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E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3270
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E_coul = 26786.2252 E_long = -33906.1028 Press = -648.6625
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---------------- Step 150 ----- CPU = 1.8576 (sec) ----------------
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TotEng = -5287.2845 KinEng = 1098.6039 Temp = 273.0740
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PotEng = -6385.8883 E_bond = 17.4924 E_angle = 32.8594
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E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9699
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E_coul = 26716.7972 E_long = -33906.8217 Press = -333.1793
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 2.18836e-07
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6 0.997 1.50913e-07
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8 1.08 6.58567e-08
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10 1.111 5.56674e-07
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12 1.08 1.99344e-07
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14 0.96 0
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18 0.957201 3.59691e-06
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31 104.52 0.000388135
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---------------- Step 200 ----- CPU = 2.4670 (sec) ----------------
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TotEng = -5308.4506 KinEng = 1100.5139 Temp = 273.5487
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PotEng = -6408.9645 E_bond = 18.2714 E_angle = 33.3035
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E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3197
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E_coul = 26735.6532 E_long = -33901.9330 Press = -1470.4761
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---------------- Step 250 ----- CPU = 3.0966 (sec) ----------------
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TotEng = -5294.1811 KinEng = 1071.1657 Temp = 266.2538
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PotEng = -6365.3467 E_bond = 14.2024 E_angle = 39.1969
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E_dihed = 19.4546 E_impro = 3.1388 E_vdwl = 753.6297
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E_coul = 26713.2917 E_long = -33908.2610 Press = -187.7499
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.78101e-06
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6 0.997001 3.51215e-06
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8 1.08 2.09172e-06
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10 1.111 5.64082e-06
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12 1.08 2.10195e-06
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14 0.96 0
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18 0.957202 7.62685e-06
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31 104.52 0.000805946
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---------------- Step 300 ----- CPU = 3.7318 (sec) ----------------
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TotEng = -5251.4403 KinEng = 1123.4658 Temp = 279.2538
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PotEng = -6374.9062 E_bond = 14.2235 E_angle = 38.4663
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E_dihed = 18.1383 E_impro = 2.3705 E_vdwl = 715.5987
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E_coul = 26744.9572 E_long = -33908.6606 Press = -467.2532
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Loop time of 3.73245 on 4 procs for 300 steps with 2004 atoms
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Pair time (%) = 2.12079 (56.8203)
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Bond time (%) = 0.00990421 (0.265354)
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Kspce time (%) = 0.742123 (19.883)
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Neigh time (%) = 0.263512 (7.06005)
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Comm time (%) = 0.334954 (8.97411)
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Outpt time (%) = 0.0165711 (0.443974)
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Other time (%) = 0.244595 (6.55321)
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FFT time (% of Kspce) = 0.225012 (30.3201)
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FFT Gflps 3d (1d only) = 0.731134 5.70596
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Nlocal: 501 ave 508 max 490 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Nghost: 6586.25 ave 6628 max 6548 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 177008 ave 180557 max 170209 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Total # of neighbors = 708030
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Ave neighs/atom = 353.308
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 26
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Dangerous builds = 0
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