[gmx-users] g(r) does not go to 1 at long r -- bug in g_rdf?

David van der Spoel spoel at xray.bmc.uu.se
Fri Nov 16 09:32:02 CET 2012

On 2012-11-16 09:12, Pablo Englebienne wrote:
> Hi,
> I tried to calculate the radial distribution functions for a simple
> system: a 5nm a side cubic box with 10 Ne atoms and 10 Ar atoms,
> simulated for 100ns in NVT @ 300K. I was expecting to get an RDF with a
> peak, stabilizing to 1.0 at long distances.
> This was the case for the Ne-Ar RDF, but not for the Ne-Ne or Ar-Ar
> RDFs, which stabilize to about 0.9. I believe this is due to a problem
> in the normalization of the histograms with respect to the number of
> pairs available: there are N*N pairs for the Ne-Ar, while N*(N-1) for
> the Ne-Ne and Ar-Ar case.
> Did somebody else find an issue like this? I think that the issue may
> become not evident for a relatively large system, as N*N ~ N*(N-1) for
> large N.
> I put the relevant files if somebody wishes to reproduce it here:
> https://gist.github.com/4085292
> I'll appreciate input on this and I can also file a bug if deemed
> necessary.
> Take care,
> Pablo
Thanks for reporting. Can you please make a redmine issue of this and 
assign it to me?

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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