[gmx-users] Coordination number

Dallas Warren Dallas.Warren at monash.edu
Wed Aug 21 00:50:40 CEST 2013

Peak can be higher, but if it is narrower the total area can still be less.  Remember it is an area under the curve.  Additionally, that overall system / box density that you are using may be different too, so that will make a difference.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Venkat Reddy
> Sent: Monday, 19 August 2013 8:11 PM
> To: Discussion list for GROMACS users
> Subject: [gmx-users] Coordination number
> Dear Gromacs Users,
> I have a query about the g_rdf utility. I have two different systems of
> water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf using
> g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn
> rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com
> where rdf1/rdf2 is for water distribution around Ionic liquid 1/2,
> the rdf1.xvg clearly shows a higher first peak g(r) than the rdf2.xvg.
> Both
> also have minima at the same distance. However, the coordination number
> at
> first minima from rdf1_cn.xvg is lesser than the same from rd2_cn.xvg.
> How
> is this possible? If the peak is larger, the integration of it should
> give
> a higher value right?
> Please help.
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
> --
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