[gmx-users] Ion binding to DNA

[soumadwip ghosh]

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