[gmx-users] RDF of water

Justin Lemkul jalemkul at vt.edu
Wed Jul 31 17:16:38 CEST 2013

On 7/31/13 10:49 AM, George Patargias wrote:
> Hello
> I am trying to calculate the RDF of water with water for a 10 ns MD of
> pure SPC water simulation (3x3x3 nm box). I run g_rdf with the default
> -rdf option (atom).
> The problem is that the integration of the RDF curve up to the first
> minimum yields a zero value which is obviously not right
> Do you have any suggestions about this? Should I run g_rdf in a different
> way?

Impossible to tell without seeing the RDF itself.  If it doesn't look like 
Figure 8.3 in the manual, then you've got a problem either with the simulation 
itself or the way the RDF was calculated.  If it does, then you've got a problem 
with how you're integrating the curve.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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