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: [EMAIL PROTECTED]
To: [email protected]
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 <[EMAIL PROTECTED]>:
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: [EMAIL PROTECTED]
To: [email protected]
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 <[EMAIL PROTECTED]>:
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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