159 lines
5.6 KiB
Groff
159 lines
5.6 KiB
Groff
LAMMPS (15 Jan 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 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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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 = 0.5773 (sec) ----------------
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TotEng = -5249.2113 KinEng = 1131.3050 Temp = 281.2023
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PotEng = -6380.5163 E_bond = 12.2067 E_angle = 31.7209
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E_dihed = 18.8100 E_impro = 2.3598 E_vdwl = 658.0491
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E_coul = 26803.5868 E_long = -33907.2495 Press = -1336.8353
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SHAKE stats (type/ave/delta) on step 100
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4 1.111 1.6521e-06
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6 0.996999 2.31654e-06
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8 1.08 1.51568e-06
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10 1.111 1.39174e-06
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12 1.08 5.85504e-07
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14 0.959999 0
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18 0.9572 8.29238e-06
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31 104.52 0.000702966
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---------------- Step 100 ----- CPU = 1.1541 (sec) ----------------
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TotEng = -5275.3150 KinEng = 1068.4676 Temp = 265.5832
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PotEng = -6343.7827 E_bond = 14.4065 E_angle = 43.2073
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E_dihed = 15.2137 E_impro = 2.2954 E_vdwl = 707.1690
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E_coul = 26780.1086 E_long = -33906.1832 Press = -704.0727
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---------------- Step 150 ----- CPU = 1.7320 (sec) ----------------
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TotEng = -5332.6748 KinEng = 1078.3846 Temp = 268.0482
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PotEng = -6411.0594 E_bond = 17.2300 E_angle = 32.3882
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E_dihed = 15.0210 E_impro = 1.6123 E_vdwl = 736.4936
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E_coul = 26693.5174 E_long = -33907.3219 Press = -461.0897
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SHAKE stats (type/ave/delta) on step 200
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4 1.111 1.19442e-06
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6 0.997 7.69718e-07
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8 1.08 3.18383e-07
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10 1.111 1.47546e-06
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12 1.08 1.05056e-06
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14 0.960001 0
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18 0.957201 4.3433e-06
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31 104.52 0.000679358
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---------------- Step 200 ----- CPU = 2.3199 (sec) ----------------
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TotEng = -5338.7112 KinEng = 1098.7385 Temp = 273.1074
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PotEng = -6437.4497 E_bond = 18.0357 E_angle = 33.0096
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E_dihed = 16.7143 E_impro = 2.6629 E_vdwl = 691.5096
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E_coul = 26702.8332 E_long = -33902.2150 Press = -1518.9567
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---------------- Step 250 ----- CPU = 2.9145 (sec) ----------------
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TotEng = -5291.1131 KinEng = 1066.9455 Temp = 265.2048
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PotEng = -6358.0586 E_bond = 14.4150 E_angle = 39.3027
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E_dihed = 19.4558 E_impro = 3.0260 E_vdwl = 768.9177
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E_coul = 26703.6583 E_long = -33906.8341 Press = -21.1614
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SHAKE stats (type/ave/delta) on step 300
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4 1.111 6.90983e-07
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6 0.997 6.61301e-07
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8 1.08 4.62407e-07
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10 1.111 1.90648e-06
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12 1.08 4.71031e-07
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14 0.96 0
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18 0.957201 3.69234e-06
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31 104.52 0.000432059
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---------------- Step 300 ----- CPU = 3.5120 (sec) ----------------
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TotEng = -5255.1926 KinEng = 1134.9271 Temp = 282.1026
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PotEng = -6390.1196 E_bond = 14.5268 E_angle = 38.2726
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E_dihed = 19.1048 E_impro = 2.1050 E_vdwl = 704.1289
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E_coul = 26739.7821 E_long = -33908.0399 Press = -687.6640
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Loop time of 3.51268 on 4 procs for 300 steps with 2004 atoms
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Pair time (%) = 1.95668 (55.7032)
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Bond time (%) = 0.00983447 (0.27997)
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Kspce time (%) = 0.72315 (20.5868)
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Neigh time (%) = 0.232158 (6.60912)
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Comm time (%) = 0.305034 (8.68378)
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Outpt time (%) = 0.0197847 (0.563236)
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Other time (%) = 0.266046 (7.57388)
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FFT time (% of Kspce) = 0.192615 (26.6355)
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FFT Gflps 3d (1d only) = 0.854109 5.21854
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Nlocal: 501 ave 514 max 485 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Nghost: 6561.25 ave 6588 max 6522 min
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Histogram: 1 0 0 0 0 1 0 0 1 1
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Neighs: 176993 ave 183217 max 167958 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Total # of neighbors = 707971
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Ave neighs/atom = 353.279
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Ave special neighs/atom = 2.34032
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Neighbor list builds = 25
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Dangerous builds = 0
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