[gmx-users] how to add user-specified non-bonded interactions?

[Idriz Seferi]

Hi all,

I have a question regarding the [ pairs ] section of the gromacs topology.

I want to add additional non-bonded interactions, but from what I
understand the [ pairs ] section is for 1-4 interactions. I read somewhere
that for structure-based modelling it has been extended to include native
contacts. This is what I am interested in.

How can I add additional non-bonded interactions between atoms that are not
necessarily in 1-4 position?

Any suggestion is greatly appreciated.

Thank you