LAMMPS (22 Jan 2008 / Patchlevel 25 Jan 2008 / CMM-CG v0.97) # Solvated 5-mer peptide units real dimension 3 atom_style angle # read topology and force field read_data data.pegc12e8 1 = max bonds/atom 1 = max angles/atom orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 1 by 1 by 4 processor grid 40140 atoms 13284 bonds 12177 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of 1-4 neighbors 6 = max # of special neighbors include parm.pegc12e8 # Solvated 5-mer peptide CG force field pair_style cg/cmm 15.0 bond_style harmonic angle_style harmonic special_bonds 0.0 0.0 1.0 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of special neighbors mass 1 31.035 mass 2 44.054 mass 3 42.081 mass 4 29.062 mass 5 54.000 pair_coeff 1 1 lj9_6 0.4491 3.7130 pair_coeff 1 2 lj9_6 0.4400 3.8900 pair_coeff 1 3 lj9_6 0.3650 3.9870 pair_coeff 1 4 lj9_6 0.3800 3.8400 pair_coeff 1 5 lj12_4 0.7000 3.9500 pair_coeff 2 2 lj9_6 0.4050 4.2500 pair_coeff 2 3 lj9_6 0.3770 4.2740 pair_coeff 2 4 lj9_6 0.3700 4.1400 pair_coeff 2 5 lj12_4 0.5700 4.3100 pair_coeff 3 3 lj9_6 0.4200 4.5060 pair_coeff 3 4 lj9_6 0.3620 4.3635 pair_coeff 3 5 lj12_4 0.3400 4.4385 pair_coeff 4 4 lj9_6 0.3120 4.2210 pair_coeff 4 5 lj12_4 0.2900 4.2960 pair_coeff 5 5 lj12_4 0.8950 4.3710 bond_coeff 1 15.00 2.79 bond_coeff 2 4.900 3.28 bond_coeff 3 7.100 3.56 bond_coeff 4 6.160 3.64 bond_coeff 5 9.000 3.13 angle_coeff 1 3.000 131.0 angle_coeff 2 3.400 132.0 angle_coeff 3 3.200 146.0 angle_coeff 4 1.500 172.0 angle_coeff 5 1.190 173.0 angle_coeff 6 1.600 172.0 neighbor 2.0 bin neigh_modify delay 5 timestep 5.0 dump 1 all xtc 200 pegc12e8-1.xtc dump_modify 1 unwrap yes #dump 2 all dcd 200 pegc12e8-1.dcd unwrap #dump_modify 2 unwrap yes velocity all create 303.0 46659 mom yes rot yes dist gaussian fix 1 all nvt 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Memory usage per processor = 4.43925 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217990.7972 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254243.7577 E_bond = 4468.5931 E_angle = 3410.1642 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 105.8245 ---------------- Step 200 ----- CPU = 27.1134 (sec) ---------------- TotEng = -217991.2189 KinEng = 36188.3877 Temp = 302.4603 PotEng = -254179.6067 E_bond = 4590.3067 E_angle = 3421.2609 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262191.1742 E_coul = 0.0000 E_long = 0.0000 Press = 37.0652 ---------------- Step 400 ----- CPU = 55.8229 (sec) ---------------- TotEng = -217934.5954 KinEng = 36330.2463 Temp = 303.6459 PotEng = -254264.8418 E_bond = 4626.8916 E_angle = 3512.1639 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262403.8973 E_coul = 0.0000 E_long = 0.0000 Press = 17.4311 ---------------- Step 600 ----- CPU = 83.0111 (sec) ---------------- TotEng = -218281.8191 KinEng = 36141.0168 Temp = 302.0644 PotEng = -254422.8358 E_bond = 4628.2093 E_angle = 3492.7509 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262543.7960 E_coul = 0.0000 E_long = 0.0000 Press = 9.5773 ---------------- Step 800 ----- CPU = 110.5361 (sec) ---------------- TotEng = -218232.9755 KinEng = 36343.0623 Temp = 303.7531 PotEng = -254576.0378 E_bond = 4659.4462 E_angle = 3567.9426 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262803.4265 E_coul = 0.0000 E_long = 0.0000 Press = -9.6008 ---------------- Step 1000 ----- CPU = 137.3658 (sec) ---------------- TotEng = -218073.8055 KinEng = 36426.1635 Temp = 304.4476 PotEng = -254499.9689 E_bond = 4602.2406 E_angle = 3636.2557 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262738.4653 E_coul = 0.0000 E_long = 0.0000 Press = -11.9067 Loop time of 137.366 on 4 procs for 1000 steps with 40140 atoms Performance: 3.145 ns/day 7.631 hours/ns Pair time (%) = 59.0174 (42.9636) Bond time (%) = 0.932444 (0.678802) Neigh time (%) = 6.30874 (4.59265) Comm time (%) = 69.5999 (50.6674) Outpt time (%) = 0.0389841 (0.0283797) Other time (%) = 1.46867 (1.06916) Nlocal: 10035 ave 19552 max 532 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 11779.5 ave 18122 max 5457 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 1.19488e+06 ave 2.39205e+06 max 12991 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 4779515 Ave neighs/atom = 119.071 Ave special neighs/atom = 1.26861 Neighbor list builds = 61 Dangerous builds = 0 write_restart pegc12e8-1.restart