LAMMPS (15 Feb 2016) # 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 ... 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 ... 1 neighbor list requests 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 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 Memory usage per processor = 14.4096 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 = -845.4774 ---------------- Step 50 ----- CPU = 0.2819 (sec) ---------------- TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748 PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365 E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771 E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981 SHAKE stats (type/ave/delta) on step 100 4 1.111 7.80799e-07 6 0.997 1.06209e-06 8 1.08 6.20484e-07 10 1.111 6.23445e-07 12 1.08 2.68063e-07 14 0.96 0 18 0.957201 5.38018e-06 31 104.52 0.000502316 ---------------- Step 100 ----- CPU = 0.5649 (sec) ---------------- TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664 PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429 E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266 E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639 ---------------- Step 150 ----- CPU = 0.8549 (sec) ---------------- TotEng = -5287.2844 KinEng = 1098.6036 Temp = 273.0739 PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593 E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685 E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1895 SHAKE stats (type/ave/delta) on step 200 4 1.111 2.18836e-07 6 0.997 1.50856e-07 8 1.08 6.58343e-08 10 1.111 5.55349e-07 12 1.08 1.99243e-07 14 0.96 0 18 0.957201 3.59666e-06 31 104.52 0.000388184 ---------------- Step 200 ----- CPU = 1.1354 (sec) ---------------- TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467 PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035 E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261 E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3871 ---------------- Step 250 ----- CPU = 1.4311 (sec) ---------------- TotEng = -5294.1809 KinEng = 1071.1623 Temp = 266.2530 PotEng = -6365.3432 E_bond = 14.2022 E_angle = 39.1953 E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5412 E_coul = 26713.8465 E_long = -33908.7226 Press = -188.8077 SHAKE stats (type/ave/delta) on step 300 4 1.111 3.78266e-06 6 0.997001 3.50137e-06 8 1.08 2.09322e-06 10 1.111 5.64331e-06 12 1.08 2.10401e-06 14 0.96 0 18 0.957202 7.67991e-06 31 104.52 0.000806336 ---------------- Step 300 ----- CPU = 1.7306 (sec) ---------------- TotEng = -5251.4350 KinEng = 1123.6256 Temp = 279.2935 PotEng = -6375.0606 E_bond = 14.2249 E_angle = 38.4712 E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4557 E_coul = 26745.4100 E_long = -33909.1249 Press = -469.5450 Loop time of 1.73061 on 4 procs for 300 steps with 2004 atoms Performance: 29.955 ns/day, 0.801 hours/ns, 173.349 timesteps/s 99.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2122 | 1.2332 | 1.2511 | 1.6 | 71.26 Bond | 0.0012589 | 0.0043506 | 0.007498 | 4.2 | 0.25 Kspace | 0.1673 | 0.18692 | 0.20947 | 4.0 | 10.80 Neigh | 0.17076 | 0.17102 | 0.17129 | 0.0 | 9.88 Comm | 0.068879 | 0.070616 | 0.071993 | 0.5 | 4.08 Output | 0.00030756 | 0.00032926 | 0.00038385 | 0.2 | 0.02 Modify | 0.059337 | 0.059592 | 0.059881 | 0.1 | 3.44 Other | | 0.004566 | | | 0.26 Nlocal: 501 ave 508 max 490 min Histogram: 1 0 0 0 0 0 1 1 0 1 Nghost: 6586.25 ave 6628 max 6548 min Histogram: 1 0 1 0 0 0 1 0 0 1 Neighs: 177007 ave 180562 max 170212 min Histogram: 1 0 0 0 0 0 0 1 1 1 Total # of neighbors = 708028 Ave neighs/atom = 353.307 Ave special neighs/atom = 2.34032 Neighbor list builds = 26 Dangerous builds = 0 Total wall time: 0:00:01