LAMMPS (20 Mar 2014-ICMS) WARNING: OMP_NUM_THREADS environment is not set. (../comm.cpp:100) 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 1 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 group peptide type <= 12 84 atoms in group peptide group one id 2 4 5 6 4 atoms in group one group two id 80 82 83 84 4 atoms in group two group ref id 37 1 atoms in group ref group colvar union one two ref 9 atoms in group colvar fix 1 all nvt temp 275.0 275.0 100.0 tchain 1 fix 3a one spring couple ref 100.0 0.0 0.0 0.0 10.0 fix 3b two spring couple ref 100.0 0.0 0.0 0.0 10.0 fix 2a ref setforce 0.0 0.0 0.0 fix 4 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 dump 1 colvar custom 1 dump.spring.lammpstrj id xu yu zu fx fy fz dump_modify 1 sort id variable sp equal f_3a+f_3b thermo_style custom step temp etotal pe ke epair ebond v_sp thermo 10 run 100 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 = 6776 1800 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 = 11.5952 Mbytes Step Temp TotEng PotEng KinEng E_pair E_bond sp 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 292.14604 10 305.06198 -5058.89 -6286.1848 1227.2948 -6413.0968 58.849896 103.38344 20 311.00591 -4999.0544 -6250.2623 1251.2079 -6417.0983 47.695275 36.699706 30 314.22398 -4993.6951 -6257.8496 1264.1545 -6421.9641 35.344161 10.563914 40 297.87525 -5020.8339 -6219.2158 1198.3819 -6389.8501 27.7232 3.8354396 50 304.02085 -5056.2539 -6279.3602 1223.1063 -6456.8181 55.459511 0.20679816 60 285.92595 -5104.0436 -6254.3523 1150.3087 -6435.5793 32.767289 0.69356527 70 277.83498 -5163.9751 -6281.733 1117.7579 -6447.7013 39.627151 11.433633 80 267.51476 -5206.4042 -6282.6428 1076.2386 -6456.6353 31.611841 6.3553235 90 278.15512 -5245.383 -6364.4289 1119.0458 -6499.8037 28.849902 0.36938816 SHAKE stats (type/ave/delta) on step 100 4 1.11098 8.97185e-05 6 0.996996 1.00569e-05 8 1.08 6.02346e-06 10 1.111 1.84257e-05 12 1.08 7.27136e-06 14 0.959996 0 18 0.957198 3.36078e-05 31 104.52 0.00306008 100 260.10505 -5292.689 -6339.1176 1046.4286 -6471.6693 25.361881 0.21986866 Loop time of 1.07153 on 2 procs for 100 steps with 2004 atoms 98.1% CPU use with 2 MPI tasks x 1 OpenMP threads Performance: 16.126 ns/day 1.488 hours/ns 93.325 timesteps/s MPI task timings breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76688 | 0.77633 | 0.78579 | 1.1 | 72.45 Bond | 0.0024021 | 0.0025222 | 0.0026424 | 0.2 | 0.24 Kspace | 0.095468 | 0.10394 | 0.1124 | 2.6 | 9.70 Neigh | 0.13518 | 0.13518 | 0.13519 | 0.0 | 12.62 Comm | 0.018154 | 0.018954 | 0.019754 | 0.6 | 1.77 Output | 0.005975 | 0.0066451 | 0.0073152 | 0.8 | 0.62 Modify | 0.025297 | 0.025306 | 0.025314 | 0.0 | 2.36 Other | | 0.002651 | | | 0.25 Nlocal: 1002 ave 1013 max 991 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 8629.5 ave 8641 max 8618 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 354118 ave 356534 max 351703 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 708237 Ave neighs/atom = 353.412 Ave special neighs/atom = 2.34032 Neighbor list builds = 12 Dangerous builds = 2