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

[Berk Hess]

Hi,

If you expect a dilute homogeneous distribution and you make an rdf between
a group and itself, it should go to 1-1/N.
But for for instance liquid water it would go to 1, since the (N-1)/N molecules
can sample the whole volume minus the volume of one molecule.

Berk.


Date: Thu, 8 May 2008 16:34:34 +0400
From: darth.vasya at gmail.com
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Re: g_rdf: normalization issues?

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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