LAMMPS (4 Jul 2012) # LAMMPS input file to run trial stevens model. units lj dimension 3 newton off package gpu force/neigh 1 1 -1 atom_style angle # Sets atom style to bead spring. read_data data.6beadtail # Calls data file. 3 = max bonds/atom 4 = max angles/atom orthogonal box = (-10.3 -10.3 -16.7) to (10.3 10.3 16.7) 1 by 1 by 1 MPI processor grid 10750 atoms 3500 bonds 3250 angles 3 = max # of 1-2 neighbors 3 = max # of 1-3 neighbors 5 = max # of 1-4 neighbors 7 = max # of special neighbors group lipid type 1 2 3750 atoms in group lipid bond_style fene # Sets bond forces as FENE model. bond_coeff 1 30.0 1.5 1.0 1.0 # Sets FENE parameters. angle_style harmonic # Sets chain bending forces angle_coeff 1 2.0 120.0 # 1-2-3 angle_coeff 2 2.0 105.0 # 2-3-4 or 1-2-10 angle_coeff 3 2.0 180.0 # Tails pair_style lj/cut/gpu 2.5 # Set lj interactions and cutoff. pair_coeff 1 1 1.0 1.0 pair_coeff 1 2 1.0 1.0 1.122462 # Sets repulsive cutoff. pair_coeff 1 3 1.0 1.0 pair_coeff 1 4 1.0 1.0 pair_coeff 2 2 1.0 1.0 pair_coeff 2 3 1.0 1.0 1.122462 # Sets repulsive cutoff. pair_coeff 2 4 1.0 1.0 1.122462 # Sets repulsive cutoff for antifreeze. pair_coeff 3 3 1.0 1.0 pair_coeff 3 4 1.1 1.2 pair_coeff 4 4 1.0 1.0 pair_modify shift yes # Shifts energy to 0. special_bonds lj 0.0 1.0 1.0 # No bond/pair doublecounting 3 = max # of 1-2 neighbors 3 = max # of 1-3 neighbors 5 = max # of 1-4 neighbors 7 = max # of special neighbors velocity all create 1.2 1324567 mom yes rot yes dist gaussian #Sets initial velocities. # Set Nose-Hoover ensemble. fix 1 all npt temp 1.2 1.2 5 x 0.5 0.5 5 y 0.5 0.5 5 z 0.5 0.5 5 couple xy # Zero linear momentum fix 2 lipid momentum 1 linear 1 1 1 thermo_style custom step temp press pe ke etotal lx ly lz pxx pyy pzz pxy pxz pyz dump 1 all xyz 5000 trtraj.xyz thermo 5000 restart 500000 afrestart variable ts equal 0.005 timestep ${ts} timestep 0.0050000000000000001041 neigh_modify delay 0 every 1 run 10000Memory usage per processor = 9.09309 Mbytes Step Temp Press PotEng KinEng TotEng Lx Ly Lz Pxx Pyy Pzz Pxy Pxz Pyz 0 1.2 16.409831 6.1618969 1.7998326 7.9617295 20.6 20.6 33.4 18.489639 18.591411 12.148444 0.026084611 -0.12195869 -0.10067528 5000 1.2110523 0.42571692 3.5591564 1.8164095 5.3755659 21.953665 21.953665 36.277625 0.44164057 0.43183938 0.4036708 -0.03203743 0.063012637 -0.056693192 10000 1.2047046 0.55002563 3.5093345 1.8068888 5.3162233 21.735683 21.735683 36.587284 0.53608216 0.58017244 0.53382228 0.015317429 -0.031277812 0.043726097 Loop time of 83.317 on 1 procs for 10000 steps with 10750 atoms Pair time (%) = 61.5515 (73.8762) Bond time (%) = 7.96419 (9.5589) Neigh time (%) = 1.52253 (1.8274) Comm time (%) = 1.52499 (1.83034) Outpt time (%) = 0.0189841 (0.0227854) Other time (%) = 10.7349 (12.8844) Nlocal: 10750 ave 10750 max 10750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8650 ave 8650 max 8650 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 Total # of neighbors = 0 Ave neighs/atom = 0 Ave special neighs/atom = 1.90698 Neighbor list builds = 1680 Dangerous builds = 0