[gmx-users] How to calculate van der Waals potential between a given residue and the rest of residues in the protein?
Yang Ye
leafyoung at yahoo.com
Mon Sep 1 02:48:35 CEST 2008
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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