[gmx-developers] energy distribution

Robert Vacha robert.vacha at marge.uochb.cas.cz
Wed Apr 9 09:47:49 CEST 2008

Yes indeed, I'd like to calculate histogram in energy of molecular
interactions. It's possible do it now by defining the solute molecule
and then separately all solvent molecules as energy groups, writing
interaction energies for all of them them and then making histograms,
but this is very slow and unpractical. That's why I'd like to implement
it either to the main run - (one would set in mdp input that he wants
histogram in interaction energies of some groups plus the size of
histogram grid) or in the separate script (this made sense only if it's
possible easily call some gromacs functions that would calculate the
interaction energies).



On Tue, 2008-04-08 at 18:41 +0200, Anton Feenstra wrote:
> Robert Vacha wrote:
> > Dear Developers,
> > 
> > I am interested in the calculation of the distribution of interaction
> > energies between two groups (solute and solvent), not at the time but as
> > number of molecules that interacts with certain strength. 
> > As far as I know this is not implemented in Gromacs, so I would like to
> > do that. I guess that it should not be so though because the
> > interactions are calculated anyway. Is it right? And do you think would
> > it be better to do it as modification of main run(where we can write
> > this to energy file?) or would it be better to write a separate script
> > that would run on trajectory file?
> You'd need a criterion to decide which molecules interact, which is not 
> as trivial as it sounds. Aside from that, in my mind 'interaction 
> strength' is equivalent to interaction energy. If that is what you mean,
> it sounds like a histogram in energy of molecular interactions?
> -- 
> Groetjes,
> Anton

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