[gmx-developers] energy distribution

Robert Vacha robert.vacha at marge.uochb.cas.cz
Wed Apr 9 13:50:51 CEST 2008

Sorry, I didn't write in the clearest way :( 
Do you think it would be better to write this modification in main part
of the code or as a script?
And can you help me with the place in code where I should start?


On Wed, 2008-04-09 at 13:12 +0200, Anton Feenstra wrote:
> Robert Vacha wrote:
> > Sorry, I'm not sure I understand what criterion you mean. I thought,
> > that I would do it as interaction energy is calculated and written in
> > energy file now (If energy groups are set, gromacs write in energy file
> > LJ and coulomb between the selected groups, and I would like to add the
> > histogram of the sum of LJ and coulomb). So the criterion would be just
> > presence of molecules in selected group, so for all of them the standard
> > Lennard-Jones interaction limited with cut-off plus coulomb interaction
> > with Ewald would be calculated. Of course, there could be molecules
> > which would have interaction energy equal 0, but that shoudn't be a
> > problem, right? Do you see any problem with calculating what I described
> > above?
> OK, now I see. Yes, that could be done. I mis-read your first e-mail and 
> thought you mentioned 'interacting molecules'. That would require some 
> definition of interaction, but a histogram of interaction energies would 
> not require that.
> Groetjes,
> Anton

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