[gmx-users] calculation radial concentration plots

[soumadwip ghosh]

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
IITB
India.