[gmx-users] Normalization in g_rdf

Omer Markovitch omermar at gmail.com
Tue Nov 24 13:01:46 CET 2009

On Tue, Nov 24, 2009 at 02:27, Ondrej Marsalek <ondrej.marsalek at gmail.com>wrote:

> Dear all,
> I would like to understand better the way g_rdf performs
> normalization. I have two unexpected results:
> 1) In a simple simulation of atomic ions in water in a cubic box, I
> get RDFs that clearly reach a constant value at large enough
> distances, but that value is somewhat lower than one. The simulation
> is NpT, could that be a problem for the normalization?
> g(r) should fluctuate around 1 at large distances, say 9 Angstroms for pure

> 2) In a simulation in a dodecahedron, I get an unexpected decrease in
> the RDF at larger distances (for free ions in solution). Is there some
> know problem with normalization in triclinic cells? Is the RDF perhaps
> not truncated "soon" enough?
Try calculating it for much larger distances, if you have PBC this should
not be a problem even with the current docecahedron.

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