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.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
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