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

[Vasilii Artyukhov]

Thanks!

Ok, so just to be clear, should I expect my RDF to go to 1 or 1-1/N at a
sufficiently large range?

2008/5/8 Berk Hess <gmx3 at hotmail.com>:

> Hi,
>
> The integrated rdf's never go to 1, since your box has corners which fall
> out of a sphere.
> The normalization should be ok.
> Some time ago the normalization was slightly different, g_rdf normalized
> with the number
> of atoms - 1, if both groups were identical. I removed this in, I think,
> 3.3.2.
>
> Berk.
>
>
>
> ------------------------------
> Date: Thu, 8 May 2008 15:18:47 +0400
> From: darth.vasya at gmail.com
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Re: g_rdf: normalization issues?
>
>
> 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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