# input script for topotools tutorial step 2b units real boundary p p p atom_style full #interaction styles pair_style lj/cut/coul/cut 12.0 bond_style harmonic angle_style harmonic dihedral_style opls pair_modify mix geometric tail yes # OPLS considers 1-4 interactions with 50%. special_bonds lj/coul 0.0 0.0 0.5 read_data data.step2b # force field parameters # missing nonbonded parameters are inferred from mixing. pair_coeff 1 1 0.066 3.5 # CT pair_coeff 2 2 0.03 2.5 # HC bond_coeff 1 268.0 1.529 # CT-CT bond_coeff 2 340.0 1.09 # CT-HC angle_coeff 1 37.5 110.7 # CT-CT-HC angle_coeff 2 33.0 107.8 # HC-CT-HC dihedral_coeff 1 0.000 0.000 0.318 0.000 # HC-CT-CT-HC velocity all create 100.0 53244 dist gaussian mom no rot no group mol id 1:3 delete_atoms group mol fix 1 all nve timestep 0.24 run 100 write_data data.ethane_delete