LAMMPS (10 Jan 2012) # Rhodopsin model variable x index 1 variable y index 1 variable z index 1 units real neigh_modify delay 5 every 1 atom_style full atom_modify map hash 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 replicate $x $y $z replicate 2 $y $z replicate 2 2 $z replicate 2 2 1 orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615) 2 by 2 by 1 MPI processor grid 128000 atoms 110892 bonds 161868 angles 227316 dihedrals 4136 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 6468 = # of size 2 clusters 14532 = # of size 3 clusters 2988 = # of size 4 clusters 16932 = # 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 = 0.248586 grid = 48 60 36 stencil order = 5 RMS precision = 7.66425e-05 using double precision FFTs brick FFT buffer size/proc = 41615 25920 12915 Memory usage per processor = 146.135 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -101425.4826 KinEng = 85779.3251 Temp = 299.0304 PotEng = -187204.8077 E_bond = 10151.9760 E_angle = 43685.4968 E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537 E_coul = 827025.3556 E_long = -1080537.3749 Press = -142.3084 Volume = 1231980.1340 ---------------- Step 50 ----- CPU = 19.1088 (sec) ---------------- TotEng = -101320.2612 KinEng = 86003.4849 Temp = 299.8118 PotEng = -187323.7461 E_bond = 9887.1072 E_angle = 43346.7920 E_dihed = 20958.7034 E_impro = 908.4715 E_vdwl = -7973.4456 E_coul = 826113.1533 E_long = -1080564.5278 Press = 238.0165 Volume = 1232126.1854 ---------------- Step 100 ----- CPU = 39.1056 (sec) ---------------- TotEng = -101158.1517 KinEng = 86355.6231 Temp = 301.0394 PotEng = -187513.7747 E_bond = 10272.0700 E_angle = 43128.6453 E_dihed = 20793.9768 E_impro = 867.0826 E_vdwl = -7586.7196 E_coul = 825555.5009 E_long = -1080544.3307 Press = 15.2192 Volume = 1232535.8453 Loop time of 39.1057 on 4 procs for 100 steps with 128000 atoms Pair time (%) = 27.0353 (69.1339) Bond time (%) = 1.5462 (3.9539) Kspce time (%) = 4.17715 (10.6817) Neigh time (%) = 4.37974 (11.1997) Comm time (%) = 0.208052 (0.532026) Outpt time (%) = 0.000296533 (0.000758287) Other time (%) = 1.75896 (4.49797) FFT time (% of Kspce) = 0.535835 (12.8278) FFT Gflps 3d (1d only) = 4.46931 11.0706 Nlocal: 32000 ave 32000 max 32000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 47957 ave 47957 max 47957 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 48112468 Ave neighs/atom = 375.879 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0