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-angle # Solvated 5-mer peptide CG force field pair_style lj/sdk 15.0 bond_style harmonic angle_style sdk 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 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 temp 303.0 303.0 100.0 thermo_style multi thermo 200 run 1000 Memory usage per processor = 9.68794 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -217835.8659 KinEng = 36252.9606 Temp = 303.0000 PotEng = -254088.8265 E_bond = 4468.5931 E_angle = 3565.0955 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262122.5151 E_coul = 0.0000 E_long = 0.0000 Press = 114.4952 ---------------- Step 200 ----- CPU = 2.7456 (sec) ---------------- TotEng = -217870.2208 KinEng = 36451.9852 Temp = 304.6634 PotEng = -254322.2060 E_bond = 4534.3652 E_angle = 3349.2174 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262205.7887 E_coul = 0.0000 E_long = 0.0000 Press = 39.4030 ---------------- Step 400 ----- CPU = 5.5655 (sec) ---------------- TotEng = -218169.7022 KinEng = 36263.1022 Temp = 303.0848 PotEng = -254432.8045 E_bond = 4598.1819 E_angle = 3416.3763 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262447.3627 E_coul = 0.0000 E_long = 0.0000 Press = 9.8923 ---------------- Step 600 ----- CPU = 8.3509 (sec) ---------------- TotEng = -217912.9317 KinEng = 36465.5757 Temp = 304.7770 PotEng = -254378.5074 E_bond = 4648.1881 E_angle = 3412.8346 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262439.5301 E_coul = 0.0000 E_long = 0.0000 Press = 25.6392 ---------------- Step 800 ----- CPU = 11.2052 (sec) ---------------- TotEng = -218439.8078 KinEng = 36035.8518 Temp = 301.1854 PotEng = -254475.6596 E_bond = 4557.5842 E_angle = 3438.5605 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262471.8043 E_coul = 0.0000 E_long = 0.0000 Press = -1.6281 ---------------- Step 1000 ----- CPU = 14.0956 (sec) ---------------- TotEng = -217925.0543 KinEng = 36271.3928 Temp = 303.1541 PotEng = -254196.4471 E_bond = 4624.7673 E_angle = 3487.7805 E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -262308.9949 E_coul = 0.0000 E_long = 0.0000 Press = -7.3081 Loop time of 14.0956 on 8 procs (8 MPI x 1 OpenMP) for 1000 steps with 40140 atoms Performance: 30.648 ns/day 0.783 hours/ns 70.944 timesteps/s Section | min time | avg time | max time |%total | #Thr -------------------------------------------------------------- Pair | 10.92 | 11.06 | 11.22 | 78.46 | 1.0x Bond | 0.3011 | 0.3112 | 0.3199 | 2.21 | 1.0x Neigh | 1.522 | 1.543 | 1.567 | 10.94 | 1.0x Comm | 0.696 | 0.8695 | 1.044 | 6.17 | 1.0x Output | 0.0003402 | 0.000362 | 0.0004911 | 0.00 | 1.0x Modify | 0.1941 | 0.2011 | 0.2144 | 1.43 | 1.0x Other | | 0.1113 | | 0.79 | Nlocal: 5017.5 ave 5041 max 4963 min Histogram: 1 0 0 0 0 2 1 0 1 3 Nghost: 10895.1 ave 10955 max 10838 min Histogram: 2 1 0 1 0 0 0 2 1 1 Neighs: 596997 ave 602732 max 590121 min Histogram: 1 0 1 0 1 1 1 1 1 1 Total # of neighbors = 4775973 Ave neighs/atom = 118.983 Ave special neighs/atom = 1.26861 Neighbor list builds = 59 Dangerous builds = 0 #write_restart pegc12e8-angle-1.restart