LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # 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 orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) 1 by 2 by 2 MPI processor grid reading atoms ... 2004 atoms reading velocities ... 2004 velocities scanning bonds ... 3 = max bonds/atom scanning angles ... 6 = max angles/atom scanning dihedrals ... 14 = max dihedrals/atom scanning impropers ... 1 = max impropers/atom reading bonds ... 1365 bonds reading angles ... 786 angles reading dihedrals ... 207 dihedrals reading impropers ... 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 #dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5 #dump_modify 2 pad 3 #dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5 #dump_modify 3 pad 3 #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 ... using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 estimated absolute RMS force accuracy = 0.0228209 estimated relative force accuracy = 6.87243e-05 using double precision FFTs 3d grid and FFT values/proc = 4312 960 Neighbor list info ... update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 5 5 5 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d/newton bin: standard 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 Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005 PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726 E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945 E_coul = 26772.2646 E_long = -33907.9271 Press = -837.0112 ---------------- Step 50 ----- CPU = 0.2858 (sec) ---------------- TotEng = -5247.5537 KinEng = 1132.4000 Temp = 281.4745 PotEng = -6379.9537 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3611 E_vdwl = 658.1785 E_coul = 26804.4441 E_long = -33907.7003 Press = -1331.7946 SHAKE stats (type/ave/delta) on step 100 4 1.111 7.80613e-07 6 0.997 1.06181e-06 8 1.08 6.20292e-07 10 1.111 6.23284e-07 12 1.08 2.67996e-07 14 0.96 0 18 0.957201 5.3796e-06 31 104.52 0.000502278 ---------------- Step 100 ----- CPU = 0.5744 (sec) ---------------- TotEng = -5257.9979 KinEng = 1078.0553 Temp = 267.9663 PotEng = -6336.0532 E_bond = 14.4829 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3273 E_coul = 26786.6829 E_long = -33906.5621 Press = -648.6820 ---------------- Step 150 ----- CPU = 0.8756 (sec) ---------------- TotEng = -5287.2798 KinEng = 1098.6028 Temp = 273.0737 PotEng = -6385.8826 E_bond = 17.4925 E_angle = 32.8594 E_dihed = 15.1624 E_impro = 1.6522 E_vdwl = 736.9675 E_coul = 26717.2656 E_long = -33907.2821 Press = -333.1828 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18699e-07 6 0.997 1.50563e-07 8 1.08 6.575e-08 10 1.111 5.54187e-07 12 1.08 1.9884e-07 14 0.96 0 18 0.957201 3.59627e-06 31 104.52 0.000388335 ---------------- Step 200 ----- CPU = 1.1602 (sec) ---------------- TotEng = -5308.4467 KinEng = 1100.4874 Temp = 273.5421 PotEng = -6408.9341 E_bond = 18.2714 E_angle = 33.3040 E_dihed = 16.8150 E_impro = 2.6051 E_vdwl = 686.3221 E_coul = 26736.1320 E_long = -33902.3837 Press = -1470.3400 ---------------- Step 250 ----- CPU = 1.4629 (sec) ---------------- TotEng = -5294.1567 KinEng = 1071.0938 Temp = 266.2359 PotEng = -6365.2505 E_bond = 14.2013 E_angle = 39.1996 E_dihed = 19.4585 E_impro = 3.1407 E_vdwl = 753.4589 E_coul = 26714.0043 E_long = -33908.7139 Press = -189.6068 SHAKE stats (type/ave/delta) on step 300 4 1.111 3.79043e-06 6 0.997001 3.6052e-06 8 1.08 2.09369e-06 10 1.111 5.6484e-06 12 1.08 2.10677e-06 14 0.96 0 18 0.957202 7.72579e-06 31 104.52 0.000806203 ---------------- Step 300 ----- CPU = 1.7662 (sec) ---------------- TotEng = -5251.3662 KinEng = 1123.7712 Temp = 279.3297 PotEng = -6375.1374 E_bond = 14.2206 E_angle = 38.4274 E_dihed = 18.1674 E_impro = 2.3734 E_vdwl = 715.3474 E_coul = 26745.4053 E_long = -33909.0790 Press = -471.5904 Loop time of 1.76629 on 4 procs for 300 steps with 2004 atoms Performance: 29.350 ns/day, 0.818 hours/ns, 169.847 timesteps/s 98.8% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2044 | 1.2351 | 1.2721 | 2.3 | 69.92 Bond | 0.0013924 | 0.0034139 | 0.0057151 | 3.2 | 0.19 Kspace | 0.17476 | 0.21195 | 0.2407 | 5.3 | 12.00 Neigh | 0.21273 | 0.21286 | 0.21293 | 0.0 | 12.05 Comm | 0.042942 | 0.046074 | 0.047584 | 0.9 | 2.61 Output | 0.00025845 | 0.00033492 | 0.00055695 | 0.0 | 0.02 Modify | 0.049944 | 0.051619 | 0.054278 | 0.8 | 2.92 Other | | 0.004988 | | | 0.28 Nlocal: 501 ave 508 max 490 min Histogram: 1 0 0 0 0 0 1 1 0 1 Nghost: 6587.75 ave 6632 max 6548 min Histogram: 1 0 1 0 0 0 1 0 0 1 Neighs: 177005 ave 180556 max 170207 min Histogram: 1 0 0 0 0 0 0 1 1 1 Total # of neighbors = 708020 Ave neighs/atom = 353.303 Ave special neighs/atom = 2.34032 Neighbor list builds = 26 Dangerous builds = 0 Total wall time: 0:00:01