# VARIABLES variable fname index data.naturalgraphene variable simname index datarestart_naturalrubbergraphene # Initialization units real boundary s s s atom_style full log log.${simname}.txt read_data ${fname} neighbor 5 bin neigh_modify page 10000000 one 1000000 every 2 dielectric 1.0 # potentials pair_style lj/charmm/coul/charmm 50.0 55.0 pair_coeff 1 1 0.0 2.9756 pair_coeff 1 2 1.0 3.0 pair_coeff 1 3 1.0 3.0 pair_coeff 1 4 1.0 3.0 pair_coeff 1 5 0.8 3.7 pair_coeff 1 6 0.8 3.7 pair_coeff 2 2 0.068 3.7239 pair_coeff 2 3 0.068 3.7239 pair_coeff 2 4 0.06171 3.6527 pair_coeff 2 5 0.04878 3.0558 pair_coeff 2 6 0.0459 2.9756 pair_coeff 3 3 0.068 3.7239 pair_coeff 3 4 0.06171 3.6527 pair_coeff 3 5 0.04878 3.0558 pair_coeff 3 6 0.0459 2.9756 pair_coeff 4 4 0.056 3.5814 pair_coeff 4 5 0.04427 2.9845 pair_coeff 4 6 0.04166 2.9043 pair_coeff 5 5 0.035 2.3876 pair_coeff 5 6 0.03294 2.3074 pair_coeff 6 6 0.031 2.2272 bond_style harmonic bond_coeff 1 365 1.5020 bond_coeff 2 360 1.1 bond_coeff 3 365 1.5020 bond_coeff 4 440 1.34 bond_coeff 5 309 1.1110 bond_coeff 6 0 1.5020 bond_coeff 7 222 1.53 angle_style charmm # U-B term angle_coeff 1 45 111.5 0 0.0 angle_coeff 2 36 109.0 5 1.802 angle_coeff 3 32 112.2 0 0.0 angle_coeff 4 48 123.5 0 0.0 angle_coeff 5 40 116.0 0 0.0 angle_coeff 6 0 119.5 0 0.0 angle_coeff 7 48 123.5 0 0.0 # angle_coeff 8 52 119.5 0 0.0 # angle_coeff 9 32 112.2 0 0.0 angle_coeff 10 35 110.1 22 2.179 angle_coeff 11 48 123.5 0 0.0 # angle_coeff 12 45 111.5 0 0.0 dihedral_style charmm dihedral_coeff 1 0.19 3 0 0.2 dihedral_coeff 2 0.19 3 0 0.2 dihedral_coeff 3 0.0 3 0 0.2 dihedral_coeff 4 0.12 3 0 0.2 dihedral_coeff 5 0.22 3 0 0.2 dihedral_coeff 6 0.19 3 0 0.2 dihedral_coeff 7 0.3 3 180 0.2 # dihedral_coeff 8 0.17 2 0 0.2 # dihedral_coeff 9 0.5 1 180 0.2 # dihedral_coeff 10 0.45 1 180 0.2 # dihedral_coeff 11 5.2 2 180 0.2 # * dihedral_coeff 12 0.0 3 0 0.2 dihedral_coeff 13 0.1 3 0 0.2 # dihedral_coeff 14 1.3 3 180 0.2 # dihedral_coeff 15 0.195 3 0 0.2 # special_bonds charmm group graphene id > 392 group polymer id < 393 fix rgd graphene move linear 0.0 0.0 0.0 units box dump 1 all dcd 50 c_naturalrubbersinglechaingraphene.dcd timestep 0.005 # Minimization thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp lx ly lz vol press thermo 1 min_style cg minimize 1e-20 1e-20 500000 1000000 # equilibration to 1500 K velocity polymer create 1500 12318 dist gaussian mom yes fix 1 polymer nve timestep 0.005 fix 2 polymer langevin 1500 1500 0.1 904297 thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp lx ly lz vol press thermo 200 run 1000 unfix 1 unfix 2 # equilibration to 300 K # velocity 1 create 300 12318 dist gaussian mom yes fix 1 polymer nve timestep 0.005 fix 2 polymer langevin 300 300 0.3 904297 thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp lx ly lz vol press thermo 200 run 10000 unfix 1 unfix 2 # dump_modify 1 every 100 # Minimization # reset_timestep 0 thermo 100 thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp lx ly lz vol press min_style cg minimize 1e-20 1e-20 500000 1000000 group pull id 378 379 380 381 382 383 384 385 386 387 388 389 390 391 compute inter polymer group/group graphene boundary no dump 3 all dcd 20 singlepolyisoprenepullinggraphene.dcd dump 2 all custom 20 dump.singlepolyisoprenepullinggraphene id type x y z xs ys zs mass fx fy fz vx vy vz timestep 0.005 fix 1 pull move linear 0.0 0.0 1.0 thermo_style custom step temp etotal evdwl eangle ebond edihed ecoul eimp c_inter c_inter[1] c_inter[2] c_inter[3] vol press lx ly lz pxx pyy pzz pxy pxz pyz thermo 1 run 100000 unfix 1 # write_restart ${simname}.txt unfix rgd # https://icme.hpc.msstate.edu/mediawiki/index.php/LAMMPS_Polymer for the explanation of the various aspects of code. see the movie shown below.