[gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?

[Yang Ye]

A more complete answer is that to define energy groups for this reside and rest residues respectively, generate the tpr with grompp and then use mdrun -rerun to run through the existing trajectory to obtain what you wanted.
 Regards,
Yang Ye



----- Original Message ----
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, September 1, 2008 5:37:47 AM
Subject: Re: [gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?



Limei Zhang wrote:
> Dear all,
> 
>  
> 
> Is it possible to use GROMACS function(s) to calculate the averaged van 
> der Waals potential /Coulomb potential between a given residue and the 
> rest residues in the protein during a certain time of simulation?
> 
>  

Different contributions to the potential can be analyzed by specifying the 
appropriate 'energygrps' in the .mdp file.

-Justin

> 
> Thanks,
> 
>  
> 
> LZhang
> 
> 
> ------------------------------------------------------------------------
> 
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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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