[gmx-users] Coordination number

[Dallas Warren]

I don't know how g_rdf script uses any density to calculate the cumulative number RDF, I have always calculated the RDF then done the integration myself to determine the coordination number.

You need to look at the data you have in front of you, work out the density yourself, integrate yourself etc to understand and see what is actually happening.  That would be much faster than asking here on the emailing list.

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, 26 August 2013 10:02 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Coordination number
> 
> Sir
> 
> Thank you for the reply. The higher graph is also broader and I thought
> should then give a higher coordination number. Does gromacs use the box
> density? does it not use 4*pi*r2*g(r) for calculating rdf (thats what I
> read in a paper where the authors have used gromacs for simulation and
> analyses)?where is the density coming then?
> 
> Thank you
> 
> 
> On Wed, Aug 21, 2013 at 4:20 AM, Dallas Warren
> <Dallas.Warren at monash.edu>wrote:
> 
> > 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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> 
> 
> 
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
> --
> gmx-users mailing list    gmx-users at gromacs.org
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