LAMMPS (10 Nov 2013) # Rhodopsin model newton off #package gpu force/neigh 2 2 1 package gpu force 0 0 1 variable x index 1 variable y index 1 variable z index 1 units real neigh_modify delay 5 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long/gpu 8.0 10.0 pair_modify mix arithmetic table 0 kspace_style pppm 1e-4 read_data data.rhodo 4 = max bonds/atom 18 = max angles/atom 40 = max dihedrals/atom 4 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 1 by 1 MPI processor grid 32000 atoms 32000 velocities 27723 bonds 40467 angles 56829 dihedrals 1034 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors #replicate $x $y $z fix 1 all shake 0.0001 5 0 m 1.0 a 232 1617 = # of size 2 clusters 3633 = # of size 3 clusters 747 = # of size 4 clusters 4233 = # of frozen angles #fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 fix 2 all npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0 #mtk no pchain 0 tchain 1 special_bonds charmm thermo 10 thermo_style custom step temp pe press pxx pyy pzz lx ly lz timestep 1.0 run 100 PPPM initialization ... G vector (1/distance) = 0.248835 grid = 25 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0355478 estimated relative force accuracy = 0.000107051 using double precision FFTs 3d grid and FFT values/proc = 41070 25600 Memory usage per processor = 240.997 Mbytes Step Temp PotEng Press Pxx Pyy Pzz Lx Ly Lz 0 299.03967 -46801.036 -86.883032 -293.24095 371.93646 -339.3446 55 77 72.7261 10 302.41047 -47047.267 -49.871753 -389.32706 360.18664 -120.47485 54.999974 76.999964 72.726066 20 302.23622 -47040.065 136.04806 578.3897 111.58599 -281.83152 54.999897 76.999856 72.725964 30 301.95463 -47027.419 451.52801 285.42459 792.79333 276.36611 55.00002 77.000028 72.726126 40 302.83071 -47098.885 496.24643 154.10035 590.08383 744.5551 55.000705 77.000987 72.727032 50 302.84084 -47110.537 212.11372 298.97639 142.75045 194.61432 55.001991 77.002787 72.728732 60 302.04567 -47071.781 385.93797 309.46513 120.62494 727.72383 55.00364 77.005096 72.730913 70 302.3265 -47117.128 94.108625 -161.11167 48.70668 394.73086 55.005706 77.007988 72.733645 80 302.22327 -47136.555 99.771215 352.8741 275.56053 -329.12099 55.007945 77.011123 72.736605 90 300.24742 -47027.202 -41.550824 126.71133 -73.826264 -177.53754 55.010279 77.01439 72.739691 100 301.34115 -47138.921 184.94121 13.346725 -65.952141 607.42904 55.01264 77.017697 72.742814 Loop time of 18.3508 on 1 procs for 100 steps with 32000 atoms Pair time (%) = 9.89442 (53.9181) Bond time (%) = 1.39118 (7.58101) Kspce time (%) = 2.06432 (11.2492) Neigh time (%) = 3.91904 (21.3562) Comm time (%) = 0.0239418 (0.130467) Outpt time (%) = 0.00309229 (0.016851) Other time (%) = 1.05483 (5.74815) FFT time (% of Kspce) = 0.491605 (23.8144) FFT Gflps 3d (1d only) = 1.05714 1.35303 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 48040 ave 48040 max 48040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 2.40503e+07 ave 2.40503e+07 max 2.40503e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24050290 Ave neighs/atom = 751.572 Ave special neighs/atom = 7.43187 Neighbor list builds = 5 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation