[gmx-users] Interaction energy

[Justin A. Lemkul]

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

No.  The names must correspond to valid groups in an index file.

> If yes, will this simulation take longer? Thank you

Perhaps, but certainly your energy file will be considerably larger.

-Justin

>  
> Steven
> 
>  
> 
>  
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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