LAMMPS (1 May 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 2 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 temp 275.0 275.0 100.0 tchain 1 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 = 6776 1800 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 = 10.4237 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5259.1770 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6394.0956 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 = -33929.1870 Press = -824.2248 ---------------- Step 50 ----- CPU = 1.6213 (sec) ---------------- TotEng = -5263.8807 KinEng = 1116.5196 Temp = 277.5272 PotEng = -6380.4003 E_bond = 12.2870 E_angle = 31.8720 E_dihed = 18.8502 E_impro = 2.4178 E_vdwl = 652.8259 E_coul = 26830.7440 E_long = -33929.3972 Press = -1286.6656 SHAKE stats (type/ave/delta) on step 100 4 1.111 3.156e-07 6 0.997 2.21313e-07 8 1.08 1.02104e-07 10 1.111 1.83752e-07 12 1.08 6.26124e-08 14 0.96 0 18 0.957201 3.72631e-06 31 104.52 0.000417496 ---------------- Step 100 ----- CPU = 3.3213 (sec) ---------------- TotEng = -5259.4821 KinEng = 1113.1434 Temp = 276.6880 PotEng = -6372.6254 E_bond = 13.8406 E_angle = 43.0396 E_dihed = 14.4609 E_impro = 1.4207 E_vdwl = 718.0489 E_coul = 26765.9378 E_long = -33929.3739 Press = -441.2620 ---------------- Step 150 ----- CPU = 5.0002 (sec) ---------------- TotEng = -5277.5470 KinEng = 1125.0069 Temp = 279.6368 PotEng = -6402.5539 E_bond = 17.0549 E_angle = 31.0347 E_dihed = 15.8320 E_impro = 1.9869 E_vdwl = 752.3759 E_coul = 26708.3669 E_long = -33929.2053 Press = -66.5637 SHAKE stats (type/ave/delta) on step 200 4 1.111 1.99875e-06 6 0.996999 1.37615e-06 8 1.08 1.12048e-06 10 1.111 2.13234e-06 12 1.08 1.35292e-06 14 0.96 0 18 0.9572 8.45114e-06 31 104.52 0.000695157 ---------------- Step 200 ----- CPU = 6.7004 (sec) ---------------- TotEng = -5326.4421 KinEng = 1085.6838 Temp = 269.8625 PotEng = -6412.1259 E_bond = 16.9071 E_angle = 29.0105 E_dihed = 19.7311 E_impro = 3.1157 E_vdwl = 706.4521 E_coul = 26741.9149 E_long = -33929.2573 Press = -894.1252 ---------------- Step 250 ----- CPU = 8.3976 (sec) ---------------- TotEng = -5347.9328 KinEng = 1079.9279 Temp = 268.4318 PotEng = -6427.8607 E_bond = 13.6513 E_angle = 37.1932 E_dihed = 20.2480 E_impro = 2.4498 E_vdwl = 687.5081 E_coul = 26740.4716 E_long = -33929.3829 Press = -1144.1348 SHAKE stats (type/ave/delta) on step 300 4 1.111 1.98887e-06 6 0.997001 6.29976e-07 8 1.08 9.15739e-07 10 1.111 4.86065e-06 12 1.08 1.17012e-06 14 0.96 0 18 0.957202 5.56744e-06 31 104.52 0.000611718 ---------------- Step 300 ----- CPU = 10.0978 (sec) ---------------- TotEng = -5317.7226 KinEng = 1113.8362 Temp = 276.8602 PotEng = -6431.5588 E_bond = 15.1475 E_angle = 37.4680 E_dihed = 17.0299 E_impro = 1.9180 E_vdwl = 711.6998 E_coul = 26714.5609 E_long = -33929.3828 Press = -838.2084 Loop time of 10.0979 on 2 procs for 300 steps with 2004 atoms Pair time (%) = 7.43954 (73.6743) Bond time (%) = 0.0228921 (0.226702) Kspce time (%) = 1.11241 (11.0163) Neigh time (%) = 0.706514 (6.99666) Comm time (%) = 0.412388 (4.08391) Outpt time (%) = 0.0110053 (0.108986) Other time (%) = 0.393122 (3.89312) FFT time (% of Kspce) = 0.129905 (11.6777) FFT Gflps 3d (1d only) = 1.26642 261.372 Nlocal: 1002 ave 1004 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 8689 ave 8723 max 8655 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 353970 ave 354344 max 353595 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 707939 Ave neighs/atom = 353.263 Ave special neighs/atom = 2.34032 Neighbor list builds = 24 Dangerous builds = 0