Hello, I am asked by one of the reviewers of my paper about the distribution of ions ( Mg2+) bound to a single stranded DNA as a function of simulation time at different salt concentrations. In order to do that I have calculated the RDF of ions from the closest atom of DNA using g_rdf with surf mol and res_com option at different time intervals. The first peak minima came around 5 angstrom and I calculated the number of ions in that cut-off at different time intervals with the -cn option of g_rdf. Then I am plotting it as no.of ions bound to DNA against time. what I want to ask is there anything wrong with this approach? I have referred to the work below
http://www.tandfonline.com/doi/pdf/10.1080/07391102.2012.732344 Is there some other ways ( command or tool wise ) where the calculations are more accurate as far as the ion binding approach is concerned? Thanks for your time in advance Soumadwip Ghosh Research Scholar IITB india -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.