Hi all,

I am very confused about how “special_bonds” works and how it affects the pair potential. Say I have the following input

special_bonds fene

bond_style fene

bond_coeff 1 30.0 1.5 1.0 1.0

pair_style lj/cut 1.12

pair_modify shift yes

pair_coeff 1 1 1.0 1.0 1.12

My questions are

1,

Between bonded atoms 1 and 2, since I have **“bond_coeff 1 30.0 1.5 1.0 1.0”** and

**"pair_coeff 1 1 1.0 1.0 1.12"**, am I counting nonzero LJ potential for 1 and 2 twice?

If not(i.e., if there is only one nonzero LJ), which set of the coefficients are not working? **"****bond_coeff 1 30.0 1.5 1.0 1.0"** or **“pair_coeff 1 1 1.0 1.0 1.12”**?

2,

If in the above input I do a little change

bond_coeff 1 30.0 1.5 1.0 1.0 ==> bond_coeff 1 30.0 1.5 **0.0** 1.0

Now between bonded atoms 1 and 2, are there still nonzero LJ potentials since I have

**"special_bonds fene**", **"****bond_coeff 1 30.0 1.5 0.0 1.0**"

and “**pair_coeff 1 1 1.0 1.0 1.12**” ?

How about the nonbonded atoms, are there still nonzero LJ potential?

Thanks!!!