[gmx-users] Interaction energy..

[Justin Lemkul]

On 10/5/12 10:16 AM, rama david wrote:
> Hi gromacs friends,
>
> I completed the simulation of receptor and ligand,
> I visualized the trajectory in the vmd I found  most of the time C terminal
> (ARG) interact with receptor ( 320 ASP) .
> I want to find out these interaction energy between these two residues in
> the simulation.
>
>
>
> How to find  these interaction energy????
>
> ( include the LJ and electrostatic interaction)..
>

I explained how to do this already.  You need properly set energygrps in the 
.mdp file and an index file that specifies those groups.  The quantities you 
want will then be in the .edr file like all other energy terms.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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