[gmx-users] Re: g_rdf: normalization issues?

[Vasilii Artyukhov]

Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the
molecule); still, the integrated RDF values seem to deviate from what
ithey're supposed to be...

2008/5/8 Vasilii Artyukhov <darth.vasya at gmail.com>:

> Hi,
>
> I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in
> water. What puzzles me is that sometimes in, e.g., two sequential runs, I
> get two RDF's with one of them having *uniformly* larger values than the
> other. Given the fact that the RDF should in principle be normalized, this
> seems very strange. In fact, the intergrated values of RDFs that I get seem
> smaller than 1*Rmax. How is this possible? Is this due to some finite box
> size effect or something else that I'm unaware of?
>
> Best regards, Vasilii
>
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