[gmx-users] Normalization in g_rdf

Berk Hess gmx3 at hotmail.com
Tue Nov 24 11:12:57 CET 2009


If you have N molecules with total volume which is significantly less than the unit-cell,
as is the case for ions in solvent, the RDF of the N molecules againt themselves
will converge to (N-1)/N.


> Date: Tue, 24 Nov 2009 01:27:27 +0100
> From: ondrej.marsalek at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Normalization in g_rdf
> 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?
> 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?
> If these should work better than they do for me, I will of course
> check my simulations again. I would just like to check first if this
> is to be expected.
> Thanks,
> Ondrej
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