#LAMMPS input toluene9 units real boundary p p p newton on atom_style full pair_style lj/cut/coul/long 14.0 bond_style harmonic angle_style harmonic kspace_style pppm 1e-4 read_data 0802134.toluene.dat pair_modify shift yes mix arithmetic special_bonds charmm #1-2,1-3,1-4 interactions set to 0.0 weighting # (as per paper) neighbor 2.0 bin neigh_modify delay 5 #neigh_modify exclude molecule all delete_bonds all multi thermo_style custom step cpu temp etotal press vol thermo 1000 thermo_modify flush yes variable vcomx equal vcm(all,x) variable vcomy equal vcm(all,y) variable vcomz equal vcm(all,z) variable amomx equal angmom(all,x) variable amomy equal angmom(all,y) variable amomz equal angmon(all,z) fix print_vcom all print 100 "${vcomx} ${vcomy} ${vcomz}" file 0802134.toluene.vcom #fix constnvt all nvt temp 298.0 298.0 100.0 tchain 1 fix fixr all rigid/nvt molecule temp 298.0 298.0 100.0 #tparam 1 1 3 #compute rdf all rdf 100 1 1 1 2 1 3 1 4 1 5 2 2 2 3 2 4 2 5 3 3 3 4 3 5 4 4 4 5 5 5 #compute msd all msd/molecule dump atomdump all custom 5000 0802134.toluene.lammpstrj id type mol x y z ix iy iz #dump atomdump2 all custom 5000 0802134.toluene.pbc.lammpstrj id type x y z fix comdump all ave/time 5000 1 5000 f_fixr[1] f_fixr[2] f_fixr[3] f_fixr[13] f_fixr[14] f_fixr[15] file 0802134.toluenecom.out mode vector restart 100000 0802134.toluene.restart #fix fixcom all recenter 0.5 0.5 0.5 units fraction timestep 2.0 #velocity all create 298.0 565833 dist gaussian mom yes rot yes run 100000 velocity all zero linear #fix 1 all ave/time 100 10 2000 c_rdf file 0702135.toluene.rdf mode vector # RDF #fix 2 all ave/time 1 1 100 c_msd[4] file 0702135.toluene.msd mode vector # MSD run 18000000