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

[Justin A. Lemkul]

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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-- 
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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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