LAMMPS (9 Jan 2009) # 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 1 by 1 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 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 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 brick FFT buffer size/proc = 41070 25600 12321 Memory usage per processor = 124.369 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2081 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0393 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207021.6578 E_long = -270399.5000 Press = -142.6055 Volume = 307995.0335 ---------------- Step 50 ----- CPU = 37.1470 (sec) ---------------- TotEng = -25330.0565 KinEng = 21501.0002 Temp = 299.8229 PotEng = -46831.0567 E_bond = 2471.7010 E_angle = 10836.4978 E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2861 E_coul = 206793.4380 E_long = -270406.1593 Press = 237.6633 Volume = 308031.6776 ---------------- Step 100 ----- CPU = 75.1354 (sec) ---------------- TotEng = -25290.7382 KinEng = 21592.0112 Temp = 301.0920 PotEng = -46882.7493 E_bond = 2567.9820 E_angle = 10781.9426 E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4962 E_coul = 206655.0353 E_long = -270400.7390 Press = 6.9485 Volume = 308134.2307 Loop time of 75.1355 on 1 procs for 100 steps with 32000 atoms Pair time (%) = 55.5501 (73.9332) Bond time (%) = 2.72528 (3.62716) Kspce time (%) = 6.11772 (8.14225) Neigh time (%) = 8.37398 (11.1452) Comm time (%) = 0.206403 (0.274708) Outpt time (%) = 0.000414848 (0.000552134) Other time (%) = 2.1616 (2.87694) FFT time (% of Kspce) = 0.43406 (7.09513) FFT Gflps 3d (1d only) = 1.19729 1.73014 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 47958 ave 47958 max 47958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12028097 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0