[gmx-users] radial density profile

gromacs query gromacsquery at gmail.com
Sat Dec 19 20:48:32 CET 2015


 Am wondering how you can have an 'axis' for single stranded DNA
simulation? ssDNA should collapse quickly if starting from helical type
configuration unless you are considering only one strand from ds-DNA or
some restraints or very small ss fragment. If you are using RDF then I
assume your single strand of DNA is not 'straight' anymore. But if its kind
a straight one then cylindrical shell grids may be used instead of radial
shells (which I think RDF constructs). So may be radial shells are not good
in this case. Depends what and where you want to calculate the ions.

You may like to use CANION from Richard Lavery's lab, though I never used
it but sounds quite promising which can give you local Molar concenrations
along DNA strand.

On Sat, Dec 19, 2015 at 10:53 AM, soumadwip ghosh <soumadwipghosh at gmail.com>

> Hi all,
>         I am looking for a way to calculate the radial density distribution
> of ions surrounding A single stranded DNA axis. Is there a way to calculate
> it using g_rdf or some other tool?
> I am thinking of taking the g(r) profile and divide it by the volume
> element 2*pi*r*h*dr ( where r is the distance values in the x axis, h is
> the length of the DNA axis) then probably converting it into a
> concentration profile expressed in terms of molarity. I hope the
> distribution should converge if the analysis is correct.
> Any thoughts on this? Can someone suggest an alternative and more precise
> method?
> Many thanks in advance.
> Soumadwip Ghosh
> Research Fellow
> Mumbai
> India
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