[gmx-users] ASP-LIG Interaction Energy : MDRUN

[Justin A. Lemkul]

nahren manuel wrote:
> Dear Gromacs Users,
>  
> I have just completed one (5ns ) mdrun.
>  
> Now If i want to calculate the interaction energy between two residues, 
> my ligand and ASP104, how should I go about calculating the same.
>  
> The one option I know is by creating .ndx . But I did not expect this 
> residue to play an important role when i started my simulation. So i did 
> not include this protein residue ASP104 as a seperate group.
>  

What you're looking for is mdrun -rerun.  Make the appropriate index groups, and 
include them in your .mdp as energy-grps when creating a new .tpr file.  I think 
you will also need to set nstenergy = 1 in the new .mdp file for the re-run.

-Justin

> Kindly advice.
>  
> regards,
> nahren
> 
> 
> 
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-- 
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Justin A. Lemkul
Graduate Research Assistant
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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