LAMMPS (21 Dec 2011-ICMS) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide units real dimension 3 atom_style angle # enforce that in z-direction there is only one # processor (could be two) for optimal performance processors * * 1 # 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) 4 by 2 by 1 MPI 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 lj/sdk 15.0 bond_style harmonic angle_style harmonic special_bonds lj/coul 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 3.0 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 temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Memory usage per processor = 10.0915 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 = 2.8323 (sec) ---------------- TotEng = -218203.1886 KinEng = 36162.5201 Temp = 302.2441 PotEng = -254365.7087 E_bond = 4568.6683 E_angle = 3409.8838 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262344.2608 E_coul = 0.0000 E_long = 0.0000 Press = 29.3660 ---------------- Step 400 ----- CPU = 5.8481 (sec) ---------------- TotEng = -217955.7366 KinEng = 36340.4946 Temp = 303.7316 PotEng = -254296.2312 E_bond = 4621.0208 E_angle = 3512.1547 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262429.4067 E_coul = 0.0000 E_long = 0.0000 Press = 16.4419 ---------------- Step 600 ----- CPU = 8.8857 (sec) ---------------- TotEng = -218291.9151 KinEng = 36079.2122 Temp = 301.5478 PotEng = -254371.1273 E_bond = 4626.3494 E_angle = 3476.1668 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262473.6435 E_coul = 0.0000 E_long = 0.0000 Press = 14.0304 ---------------- Step 800 ----- CPU = 11.9061 (sec) ---------------- TotEng = -218539.5667 KinEng = 36042.0419 Temp = 301.2372 PotEng = -254581.6086 E_bond = 4563.0010 E_angle = 3616.1814 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262760.7910 E_coul = 0.0000 E_long = 0.0000 Press = -6.8312 ---------------- Step 1000 ----- CPU = 14.9738 (sec) ---------------- TotEng = -217783.9370 KinEng = 36453.9620 Temp = 304.6800 PotEng = -254237.8990 E_bond = 4693.8725 E_angle = 3528.1925 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262459.9639 E_coul = 0.0000 E_long = 0.0000 Press = 0.0980 Loop time of 14.9738 on 8 procs (8 MPI x 1 OpenMP) for 1000 steps with 40140 atoms Performance: 28.850 ns/day 0.832 hours/ns 66.783 timesteps/s Section | min time | avg time | max time |%total | #Thr -------------------------------------------------------------- Pair | 11.92 | 12.15 | 12.39 | 81.13 | 1.0x Bond | 0.2939 | 0.3141 | 0.3283 | 2.10 | 1.0x Neigh | 1.068 | 1.09 | 1.119 | 7.28 | 1.0x Comm | 0.8103 | 1.091 | 1.341 | 7.29 | 1.0x Output | 0.0003598 | 0.0003798 | 0.0005069 | 0.00 | 1.0x Modify | 0.1976 | 0.2041 | 0.2086 | 1.36 | 0.9x Other | | 0.1261 | | 0.84 | Nlocal: 5017.5 ave 5051 max 4982 min Histogram: 1 2 0 0 1 0 1 1 0 2 Nghost: 11697.4 ave 11771 max 11645 min Histogram: 3 0 0 0 2 1 0 1 0 1 Neighs: 711460 ave 720454 max 704238 min Histogram: 2 1 1 0 0 1 1 1 0 1 Total # of neighbors = 5691680 Ave neighs/atom = 141.796 Ave special neighs/atom = 1.26861 Neighbor list builds = 38 Dangerous builds = 0 #write_restart pegc12e8-1.restart