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: >>> lecielll@googlemail.**com <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<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >> > >
<<attachment: RDF- CC.png>>
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