LAMMPS (27 Mar 2011) # 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 2 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 = 4312 960 3696 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 = 10.6052 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5237.4579 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6372.3765 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 = -33907.4679 Press = -845.4762 ---------------- Step 50 ----- CPU = 0.5035 (sec) ---------------- TotEng = -5247.5491 KinEng = 1132.4011 Temp = 281.4748 PotEng = -6379.9502 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1770 E_coul = 26803.9897 E_long = -33907.2410 Press = -1331.7985 SHAKE stats (type/ave/delta) on step 100 4 1.111 7.80799e-07 6 0.997 1.06209e-06 8 1.08 6.20484e-07 10 1.111 6.23444e-07 12 1.08 2.68063e-07 14 0.96 0 18 0.957201 5.38017e-06 31 104.52 0.000502314 ---------------- Step 100 ----- CPU = 1.0089 (sec) ---------------- TotEng = -5257.9973 KinEng = 1078.0555 Temp = 267.9664 PotEng = -6336.0528 E_bond = 14.4828 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266 E_coul = 26786.2248 E_long = -33906.1028 Press = -648.6626 ---------------- Step 150 ----- CPU = 1.5261 (sec) ---------------- TotEng = -5287.2844 KinEng = 1098.6039 Temp = 273.0740 PotEng = -6385.8883 E_bond = 17.4924 E_angle = 32.8593 E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685 E_coul = 26716.7990 E_long = -33906.8220 Press = -333.1910 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18836e-07 6 0.997 1.50835e-07 8 1.08 6.58286e-08 10 1.111 5.55388e-07 12 1.08 1.99221e-07 14 0.96 0 18 0.957201 3.59665e-06 31 104.52 0.000388185 ---------------- Step 200 ----- CPU = 2.0277 (sec) ---------------- TotEng = -5308.4533 KinEng = 1100.5081 Temp = 273.5473 PotEng = -6408.9613 E_bond = 18.2714 E_angle = 33.3035 E_dihed = 16.8150 E_impro = 2.6054 E_vdwl = 686.3253 E_coul = 26735.6522 E_long = -33901.9341 Press = -1470.4128 ---------------- Step 250 ----- CPU = 2.5482 (sec) ---------------- TotEng = -5294.1793 KinEng = 1071.1639 Temp = 266.2534 PotEng = -6365.3432 E_bond = 14.2022 E_angle = 39.1951 E_dihed = 19.4554 E_impro = 3.1386 E_vdwl = 753.5442 E_coul = 26713.3849 E_long = -33908.2636 Press = -188.7520 SHAKE stats (type/ave/delta) on step 300 4 1.111 3.78179e-06 6 0.997001 3.49518e-06 8 1.08 2.09281e-06 10 1.111 5.64213e-06 12 1.08 2.10337e-06 14 0.96 0 18 0.957202 7.67601e-06 31 104.52 0.000806295 ---------------- Step 300 ----- CPU = 3.0773 (sec) ---------------- TotEng = -5251.4367 KinEng = 1123.6267 Temp = 279.2938 PotEng = -6375.0634 E_bond = 14.2250 E_angle = 38.4733 E_dihed = 18.1306 E_impro = 2.3699 E_vdwl = 715.4580 E_coul = 26744.9481 E_long = -33908.6682 Press = -469.4697 Loop time of 3.07745 on 4 procs for 300 steps with 2004 atoms Pair time (%) = 1.94511 (63.2051) Bond time (%) = 0.00942487 (0.306256) Kspce time (%) = 0.515528 (16.7518) Neigh time (%) = 0.224395 (7.29158) Comm time (%) = 0.221778 (7.20655) Outpt time (%) = 0.00817496 (0.26564) Other time (%) = 0.153044 (4.97309) FFT time (% of Kspce) = 0.0852013 (16.527) FFT Gflps 3d (1d only) = 1.93089 6.56039 Nlocal: 501 ave 508 max 490 min Histogram: 1 0 0 0 0 0 1 1 0 1 Nghost: 6586.25 ave 6628 max 6548 min Histogram: 1 0 1 0 0 0 1 0 0 1 Neighs: 177009 ave 180567 max 170213 min Histogram: 1 0 0 0 0 0 0 1 1 1 Total # of neighbors = 708037 Ave neighs/atom = 353.312 Ave special neighs/atom = 2.34032 Neighbor list builds = 26 Dangerous builds = 0