[gmx-users] Interaction energy

Steven Neumann s.neumann08 at gmail.com
Tue Oct 18 09:44:55 CEST 2011

On Mon, Oct 17, 2011 at 6:02 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> Steven Neumann wrote:
>> Dear Gmx Users,
>>  I would like to calculate the interaction energy (LJ and electrostatic)
>> between each residue and my ligands (10 ligands in the system). I would like
>> to see what is the contribution of electrostatic and vdW interactions
>> between ligand and each of my residue. I thought to use g_energy and specify
>> each of my residues in index files but it is not possible. Will you suggest
>> how to do this?
> For such information, you have to specify these groups as energygrps in the
> .mdp file.  You can rerun the trajectory using mdrun -rerun and a new .tpr
> file specifying these groups, but depending on the output frequency, the
> result may not be as accurate as you'd like.
> -Justin
Thank you Justin. Now I have two groups sepcified in my mdp file:

energygrps = Protein LIG

How can I specify each residue of my protein separately and each ligand? In
my md.gro file I have residues:

> 91GLY 92TYR ..... 161LIG 162LIG...

Will it be correct like this

energygrps = 91GLY 92 TYR ... 161LIG 162LIG...

If yes, will this simulation take longer? Thank you

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