[gmx-users] what does g_energy actually calculate?

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 30 19:48:22 CEST 2005

On Tue, 2005-08-30 at 12:21 +0100, Robert d'Rozario wrote:
> Hi
> I have calculated the energy between three amino acids in my protein using
> rerun
> and was wondering what g_energy actually calculates? I was hoping to get the
> short range coloumbic interaction energy between these three residues but
> have
> noticed that when these residues move to greater than my cutoff, the energy
> does
> not drop off to 0. So am I right in assuming that g_energy works by
> calculating
> the short range interactions of each residue with anything within the cutoff
> rather than just interaction between the residues you have specified to
> be in
> the energy group.
If your mdp file and index file are correct you will get a matrix of all
interactions in the energy file for your rerun.
> Thanks
> Rob
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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