[gmx-users] specifying interaction energy between residues

[Mark Abraham]

----- Original Message -----
From: Gene Polovy <gpolovy at gmail.com>
Date: Saturday, May 22, 2010 8:37
Subject: [gmx-users] specifying interaction energy between residues
To: gmx-users at gromacs.org

> Hi There,
> 
> I'm trying to run a course grained (c alpha) simulation of a 

Letting us know more about what kind of coarse-grained model you're trying to modify would be useful.

> 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!

Ah, but we're not sure what your vanilla model is, so it's hard to advise...

Mark