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.war...@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.war...@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-boun...@gromacs.org [mailto:gmx-users- > > boun...@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 > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- 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@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
