[gmx-users] how to remove an energy contribution in gromacs?

Jones de Andrade johannesrs at gmail.com
Mon Aug 6 15:26:06 CEST 2007

Hi Mark.

Thanks a lot, first of all.  ;)

Unfortunatelly, the suggestion will not work: as you mentioned, there is a
limit for 256 molecules, and my systems are composed by at least 500.

Moreover, I still don't see any reason why the nexcl could affect the bond,
angle nd dihedrals energy outputs. :(

Any other thoughts?

Thanks a lot,


On 8/6/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Jones de Andrade wrote:
> > Hi all.
> >
> > Well, I'm trying to calculate an <E> energy from my simulations, where
> > <E> here stands only for the sum of *intermolecular* vdw and coulombic
> > terms, and LJ(1-4) and coul(1-4). This means that I should find a way to
> > exclude any "1-5", "1-6", "1-7" and so on contributions for coulombic
> > and vdw energies, which I guess are included in the SR terms if the rcut
> > is long enough.
> If you define each molecule as an energy group, then GROMACS will report
> all the self vdW and Coulomb terms, and all pairwise terms and you can
> add up whatever ones you want. This won't work if you have more than 256
> molecules, though.
> Mark
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