[gmx-users] RDF calculation.

[soumadwip ghosh]

Hi,
    I am studying the dynamics of a double stranded DNA in presence of
small molecules. I want to study the preferential binding of these
molecules in the grooves and backbones of the DNA and also calculate the
feasibility of these binding in terms of calculating the free energy
change.My question is-

1. while calculating radial distribution functions say between DNA minor
groove and choline, should I consider the center-off-mass atom of the minor
groove by using the -COM option of g_rdf?

2. Do you think calculation of PMF from g(r) for a specific ion binding
with the DNA can provide reliable free energy change or do I have to switch
to umbrella sampling?

PS: I only want to investigate the small molecule binding, not the
stability of the DNA duplex as a whole.

Thanks for your time in advance.

Soumadwip Ghosh
Research Fellow
Indian Institute of Technology Bombay
India