Hey, This is just exactly what you'd expect for polymer chains in a solution (suspension?). From the closest neighbours the fine structure, the discrete distribution of carbon atoms, is still seen, but for those further away it's blurred. Dallas' excercise should be a fine way to show that more explicitly.
Cheers, Tsjerk On Fri, Sep 16, 2011 at 12:26 AM, Dallas Warren <dallas.war...@monash.edu> wrote: > Load up some frames into VMD and start measuring the distances shown by the > peaks in your RDF, link them with what you actually see in there (using > something like a transparent representation of the carbon atom(s) using VDW > then set the sphere scale so that it matches the correct radius, may be an > easier way to do this, but this would make it easy to see). Appears it may > be something real, so just check the coordinate file and see where they are > actually coming from. > > > > Catch ya, > > Dr. Dallas Warren > > Medicinal Chemistry and Drug Action > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@monash.edu > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] > On Behalf Of Moeed > Sent: Friday, 16 September 2011 12:55 AM > To: jalem...@vt.edu; Discussion list for GROMACS users > Subject: Re: [gmx-users] radial distribution function > > > > Hello again, > > I tried comparing RDF plots generated by sampling from 4 to 5 ns run and a > longer run from 4 to 30 ns to see whether the small jumps on the plot are > due to insufficient sampling. Attached is the new plot showing that two RDF > curves are almost identical. I only wanted to let you know and please > comment on the attached plot if you have any ideas. Thank you. :) > > Moeed > > On Sat, Sep 10, 2011 at 10:00 AM, Moeed <lecie...@googlemail.com> wrote: > > Thank you for your input. I am going to run for another 15 ns to see if the > little jumps vanish. > > Best, > > > > On Fri, Sep 9, 2011 at 9:16 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > lina wrote: > > > > On Sat, Sep 10, 2011 at 3:35 AM, Moeed <lecie...@googlemail.com > <mailto:lecie...@googlemail.com>> wrote: > > Dear users, > > I have created radial distribution function plot for Carbon atoms in > a system containing polymer chains. I see some little jumps between > first and second peak. > I need your help to comment on how this behavior can be justified > (or if the plot is wrong). > > g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx > Thank you in advance. > > > I think your figure is fine. > > > > I think, based on information given in subsequent messages, that there is > insufficient data collection to assess whether this RDF plot is as > meaningful as it could be. There is nothing glaringly wrong, but the > roughness is due to insufficient sampling. > > > > You just need how to proper interpret your figures, truly understand what > the "radial distribution" means. > > > > > I think it inappropriate to suggest that the OP does not understand the > concept behind the figure; some guidance, perhaps is necessary, but nothing > more. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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
