[gmx-users] specifying interaction energy between residues

[Gene Polovy]

Hi There,

I'm trying to run a course grained (c alpha) simulation of a protein and I'd like to know how/where I can define heterogeneous native interaction energies between residues. Is it under [ pairs ] in the topology file? In other words, I'd like to use a flavored model rather than a vanilla model. Please help!

Regards,

Gene