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 3 one spring couple two 100.0 0.0 0.0 0.0 10.0 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.spring2.lammpstrj id xu yu zu fx fy fz dump_modify 1 sort id thermo_style custom step temp etotal pe ke epair ebond f_3 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 3 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 273.74323 10 333.47973 -4982.3893 -6324.0116 1341.6223 -6400.417 21.367753 12.393269 20 309.56974 -4999.4934 -6244.9234 1245.43 -6401.6969 43.595447 13.004393 30 316.97689 -5025.5598 -6300.7895 1275.2297 -6422.5335 27.323113 6.7588862 40 297.55811 -5088.2155 -6285.3215 1197.106 -6395.3714 13.676871 25.625154 50 296.80002 -5117.2927 -6311.3488 1194.0561 -6451.8274 30.631277 5.3320302 60 281.72798 -5188.494 -6321.9138 1133.4198 -6427.8834 26.28765 20.573958 70 277.26045 -5224.8415 -6340.288 1115.4465 -6447.8494 27.742889 0.69414895 80 268.01458 -5281.8501 -6360.0995 1078.2495 -6496.6062 20.300729 5.260642 90 270.43384 -5334.0847 -6422.0671 1087.9824 -6563.2486 39.845992 1.183249 SHAKE stats (type/ave/delta) on step 100 4 1.11096 0.000191466 6 0.996989 3.5552e-05 8 1.08 9.10001e-06 10 1.111 1.58547e-05 12 1.08 5.80613e-06 14 0.959997 0 18 0.957198 2.92454e-05 31 104.52 0.00239929 100 260.35617 -5387.2297 -6434.6686 1047.4389 -6534.1956 20.246734 0.075048996 Loop time of 1.07264 on 2 procs for 100 steps with 2004 atoms 98.6% CPU use with 2 MPI tasks x 1 OpenMP threads Performance: 16.110 ns/day 1.490 hours/ns 93.228 timesteps/s MPI task timings breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76647 | 0.77219 | 0.77792 | 0.7 | 71.99 Bond | 0.0024974 | 0.0025403 | 0.0025833 | 0.1 | 0.24 Kspace | 0.091998 | 0.096921 | 0.10184 | 1.6 | 9.04 Neigh | 0.14764 | 0.14765 | 0.14767 | 0.0 | 13.77 Comm | 0.018904 | 0.01937 | 0.019835 | 0.3 | 1.81 Output | 0.005985 | 0.0067209 | 0.0074568 | 0.9 | 0.63 Modify | 0.024529 | 0.024536 | 0.024542 | 0.0 | 2.29 Other | | 0.002705 | | | 0.25 Nlocal: 1002 ave 1010 max 994 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 8645 ave 8652 max 8638 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 354116 ave 356373 max 351860 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 708233 Ave neighs/atom = 353.41 Ave special neighs/atom = 2.34032 Neighbor list builds = 13 Dangerous builds = 1