LAMMPS (27 Nov 2018) 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 pair_style lj/sdk 15.0 bond_style harmonic angle_style harmonic special_bonds lj/coul 0.0 0.0 1.0 read_data data.pegc12e8.gz orthogonal box = (-63.7 -63.7 -200) to (63.7 63.7 200) 1 by 1 by 1 MPI processor grid reading atoms ... 40140 atoms reading velocities ... 40140 velocities scanning bonds ... 1 = max bonds/atom scanning angles ... 1 = max angles/atom reading bonds ... 13284 bonds reading angles ... 12177 angles 2 = max # of 1-2 neighbors 2 = max # of 1-3 neighbors 4 = max # of special neighbors 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 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 18 ghost atom cutoff = 18 binsize = 9, bins = 15 15 45 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/sdk, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 47.18 | 47.18 | 47.18 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 = 11.2074 (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 = 22.6113 (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 = 34.0551 (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 = 45.5316 (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 = 56.9111 (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 56.9112 on 1 procs for 1000 steps with 40140 atoms Performance: 7.591 ns/day, 3.162 hours/ns, 17.571 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 50.775 | 50.775 | 50.775 | 0.0 | 89.22 Bond | 0.88358 | 0.88358 | 0.88358 | 0.0 | 1.55 Neigh | 4.5176 | 4.5176 | 4.5176 | 0.0 | 7.94 Comm | 0.14942 | 0.14942 | 0.14942 | 0.0 | 0.26 Output | 0.00057101 | 0.00057101 | 0.00057101 | 0.0 | 0.00 Modify | 0.4728 | 0.4728 | 0.4728 | 0.0 | 0.83 Other | | 0.1127 | | | 0.20 Nlocal: 40140 ave 40140 max 40140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 25968 ave 25968 max 25968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5.69168e+06 ave 5.69168e+06 max 5.69168e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 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 Total wall time: 0:00:57