forked from lijiext/lammps
155 lines
5.4 KiB
Groff
155 lines
5.4 KiB
Groff
LAMMPS (12 Feb 2007)
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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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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 = 0.268725
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grid = 15 15 15
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RMS precision = 4.85953e-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 = 8.89765 Mbytes
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---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
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TotEng = -5237.4579 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 = 26772.2794 E_long = -33907.9417 Press = -845.4771
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---------------- Step 50 ----- CPU = 1.0231 (sec) ----------------
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TotEng = -5247.5482 KinEng = 1132.4030 Temp = 281.4752
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PotEng = -6379.9511 E_bond = 12.2118 E_angle = 31.7365
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E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1774
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E_coul = 26804.4624 E_long = -33907.7148 Press = -1331.7939
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 7.80748e-07
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6 0.997 1.06201e-06
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8 1.08 6.20434e-07
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10 1.111 6.23399e-07
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12 1.08 2.68045e-07
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14 0.96 0
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18 0.957201 5.38002e-06
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31 104.52 0.000502303
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---------------- Step 100 ----- CPU = 2.0570 (sec) ----------------
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TotEng = -5257.9999 KinEng = 1078.0524 Temp = 267.9656
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PotEng = -6336.0523 E_bond = 14.4828 E_angle = 43.4429
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E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3271
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E_coul = 26786.6988 E_long = -33906.5767 Press = -648.6634
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---------------- Step 150 ----- CPU = 3.1067 (sec) ----------------
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TotEng = -5287.2849 KinEng = 1098.6036 Temp = 273.0739
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PotEng = -6385.8885 E_bond = 17.4924 E_angle = 32.8594
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E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9698
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E_coul = 26717.2709 E_long = -33907.2954 Press = -333.1851
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 2.18831e-07
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6 0.997 1.50909e-07
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8 1.08 6.58563e-08
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10 1.111 5.56695e-07
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12 1.08 1.99338e-07
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14 0.96 0
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18 0.957201 3.59689e-06
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31 104.52 0.000388134
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---------------- Step 200 ----- CPU = 4.1845 (sec) ----------------
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TotEng = -5308.4508 KinEng = 1100.5108 Temp = 273.5480
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PotEng = -6408.9616 E_bond = 18.2713 E_angle = 33.3035
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E_dihed = 16.8154 E_impro = 2.6052 E_vdwl = 686.3209
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E_coul = 26736.1285 E_long = -33902.4064 Press = -1470.4571
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---------------- Step 250 ----- CPU = 5.2516 (sec) ----------------
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TotEng = -5294.1865 KinEng = 1071.1626 Temp = 266.2530
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PotEng = -6365.3492 E_bond = 14.2025 E_angle = 39.1972
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E_dihed = 19.4548 E_impro = 3.1389 E_vdwl = 753.6340
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E_coul = 26713.7586 E_long = -33908.7351 Press = -187.8153
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.78173e-06
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6 0.997001 3.51761e-06
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8 1.08 2.09202e-06
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10 1.111 5.64179e-06
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12 1.08 2.10252e-06
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14 0.96 0
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18 0.957202 7.62675e-06
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31 104.52 0.00080599
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---------------- Step 300 ----- CPU = 6.3128 (sec) ----------------
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TotEng = -5251.4326 KinEng = 1123.4442 Temp = 279.2484
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PotEng = -6374.8768 E_bond = 14.2233 E_angle = 38.4644
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E_dihed = 18.1398 E_impro = 2.3706 E_vdwl = 715.6075
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E_coul = 26745.4484 E_long = -33909.1309 Press = -467.0013
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Loop time of 6.31307 on 4 procs for 300 steps with 2004 atoms
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Pair time (%) = 3.7478 (59.3657)
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Bond time (%) = 0.0190388 (0.301577)
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Kspce time (%) = 1.04423 (16.5407)
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Neigh time (%) = 0.366191 (5.80052)
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Comm time (%) = 0.669456 (10.6043)
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Outpt time (%) = 0.0110819 (0.175539)
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Other time (%) = 0.455277 (7.21165)
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FFT time (% of Kspce) = 0.219916 (21.0601)
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FFT Gflps 3d 1d-only = 0.748076 3.75246
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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 180559 max 170208 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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