[gmx-users] calculation radial concentration plots

Felipe Merino felipe.merino at mpi-dortmund.mpg.de
Wed Jul 1 10:27:26 CEST 2015


Check out RIcard Lavery's CANION, I think it'll do what you need.

There's the paper

And the software


On 01/07/15 09:31, soumadwip ghosh wrote:
> Hi all,
>           I have been asked by one of my reviewers to calculate the number
> of excess cations surrounding a DNA duplex using radial concentration of
> the ions computed by integrating the grid-based concentration data within a
> cylindrical volume surrounding the DNA . I am actually trying to obtain
> curves like that of figure 7 in the link below-
> http://onlinelibrary.wiley.com/doi/10.1002/bip.22461/epdf
> Which are obtained from the radial concentration profiles. My question is
> how to make a radial concentration profile of say tetramethylammonium
> cations from some DNA groove/ backbone atoms and then obtain curves like
> that of figure 7 using equation 2 of the above reference.
> Thanks for your help in advance.
> Soumadwip Ghosh
> Research Fellow
> India.

Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2306

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