forked from lijiext/lammps
159 lines
5.6 KiB
Groff
159 lines
5.6 KiB
Groff
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LAMMPS (10 Sep 2010)
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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 temp 275.0 275.0 100.0 tchain 1
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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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compute bnd all property/local btype batom1 batom2
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dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
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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 = 8.90402 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 = 26771.8055 E_long = -33907.4679 Press = -845.4762
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---------------- Step 50 ----- CPU = 0.5064 (sec) ----------------
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TotEng = -5247.5491 KinEng = 1132.4011 Temp = 281.4748
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PotEng = -6379.9502 E_bond = 12.2118 E_angle = 31.7365
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E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1770
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E_coul = 26803.9897 E_long = -33907.2410 Press = -1331.7985
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 7.80799e-07
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6 0.997 1.06209e-06
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8 1.08 6.20484e-07
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10 1.111 6.23444e-07
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12 1.08 2.68063e-07
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14 0.96 0
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18 0.957201 5.38017e-06
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31 104.52 0.000502314
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---------------- Step 100 ----- CPU = 1.0130 (sec) ----------------
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TotEng = -5257.9973 KinEng = 1078.0555 Temp = 267.9664
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PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429
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E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
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E_coul = 26786.2248 E_long = -33906.1028 Press = -648.6626
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---------------- Step 150 ----- CPU = 1.5303 (sec) ----------------
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TotEng = -5287.2844 KinEng = 1098.6039 Temp = 273.0740
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PotEng = -6385.8883 E_bond = 17.4924 E_angle = 32.8593
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E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
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E_coul = 26716.7990 E_long = -33906.8220 Press = -333.1910
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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 1.50835e-07
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8 1.08 6.58286e-08
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10 1.111 5.55388e-07
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12 1.08 1.99221e-07
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14 0.96 0
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18 0.957201 3.59665e-06
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31 104.52 0.000388185
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---------------- Step 200 ----- CPU = 2.0346 (sec) ----------------
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TotEng = -5308.4533 KinEng = 1100.5081 Temp = 273.5473
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PotEng = -6408.9613 E_bond = 18.2714 E_angle = 33.3035
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E_dihed = 16.8150 E_impro = 2.6054 E_vdwl = 686.3253
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E_coul = 26735.6522 E_long = -33901.9341 Press = -1470.4128
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---------------- Step 250 ----- CPU = 2.5585 (sec) ----------------
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TotEng = -5294.1793 KinEng = 1071.1639 Temp = 266.2534
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PotEng = -6365.3432 E_bond = 14.2022 E_angle = 39.1951
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E_dihed = 19.4554 E_impro = 3.1386 E_vdwl = 753.5442
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E_coul = 26713.3849 E_long = -33908.2636 Press = -188.7520
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 3.78179e-06
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6 0.997001 3.49518e-06
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8 1.08 2.09281e-06
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10 1.111 5.64213e-06
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12 1.08 2.10337e-06
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14 0.96 0
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18 0.957202 7.67601e-06
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31 104.52 0.000806295
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---------------- Step 300 ----- CPU = 3.0867 (sec) ----------------
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TotEng = -5251.4367 KinEng = 1123.6267 Temp = 279.2938
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PotEng = -6375.0634 E_bond = 14.2250 E_angle = 38.4733
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E_dihed = 18.1306 E_impro = 2.3699 E_vdwl = 715.4580
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E_coul = 26744.9481 E_long = -33908.6682 Press = -469.4697
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Loop time of 3.0868 on 4 procs for 300 steps with 2004 atoms
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Pair time (%) = 1.9579 (63.4281)
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Bond time (%) = 0.00858217 (0.278028)
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Kspce time (%) = 0.511241 (16.5622)
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Neigh time (%) = 0.225836 (7.31619)
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Comm time (%) = 0.223754 (7.24873)
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Outpt time (%) = 0.00822645 (0.266504)
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Other time (%) = 0.151261 (4.90025)
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FFT time (% of Kspce) = 0.0808918 (15.8226)
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FFT Gflps 3d (1d only) = 2.03375 6.47452
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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: 177009 ave 180567 max 170213 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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Total # of neighbors = 708037
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Ave neighs/atom = 353.312
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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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