[gmx-users] Coordination number
venkat4bt at gmail.com
Mon Aug 26 14:02:13 CEST 2013
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?
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
> > -----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
Laboratory of Computational Biophysics
Department of Biotechnology
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