LAMMPS (10 Jan 2012) # Rhodopsin model 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 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo 4 = max bonds/atom 8 = max angles/atom 18 = max dihedrals/atom 2 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 2 by 2 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 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 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector = 0.248831 grid = 25 32 32 stencil order = 5 RMS precision = 7.57143e-05 using double precision FFTs brick FFT buffer size/proc = 13230 6400 5670 Memory usage per processor = 54.4744 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030 Volume = 307995.0335 ---------------- Step 50 ----- CPU = 4.7389 (sec) ---------------- TotEng = -25330.0783 KinEng = 21501.0023 Temp = 299.8230 PotEng = -46831.0806 E_bond = 2471.7004 E_angle = 10836.4977 E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2753 E_coul = 206793.4044 E_long = -270406.1594 Press = 237.6744 Volume = 308031.5641 ---------------- Step 100 ----- CPU = 9.6394 (sec) ---------------- TotEng = -25290.7642 KinEng = 21592.0080 Temp = 301.0920 PotEng = -46882.7722 E_bond = 2567.9806 E_angle = 10781.9408 E_dihed = 5198.7431 E_impro = 216.7832 E_vdwl = -1902.4804 E_coul = 206654.9995 E_long = -270400.7390 Press = 6.9875 Volume = 308133.9900 Loop time of 9.63943 on 4 procs for 100 steps with 32000 atoms Pair time (%) = 6.60502 (68.5208) Bond time (%) = 0.375643 (3.89695) Kspce time (%) = 1.09311 (11.3399) Neigh time (%) = 1.08158 (11.2203) Comm time (%) = 0.0815379 (0.845879) Outpt time (%) = 0.000157952 (0.00163861) Other time (%) = 0.402393 (4.17445) FFT time (% of Kspce) = 0.0966156 (8.83863) FFT Gflps 3d (1d only) = 5.37903 12.4303 Nlocal: 8000 ave 8143 max 7933 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 22733.5 ave 22769 max 22693 min Histogram: 1 0 0 0 0 2 0 0 0 1 Neighs: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min Histogram: 1 2 0 0 0 0 0 0 0 1 Total # of neighbors = 12028107 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0