[gmx-users] Regarding RDF calculations

soumadwip ghosh soumadwipghosh at gmail.com
Fri Feb 27 08:00:35 CET 2015

Dear users,
                  I have a query about some reviews one a paper which I
submitted recently. It deals with the binding of molecular ions with double
stranded DNA segments. My questions are-

1. Is it customary to take into account The centre-of -mass for DNA grooves
or backbones while calculating RDF? Without that being taken into account,
what kind of artifacts are to be seen?

2. Why is it necessary to show the running co-ordination number up to the
first solvation shell? I have calculated the excess cordination number for
each ions in DNA up to half of the box length using the Kirkwood-Buff
integrals. But I think there is a confusion between running coordination
and the excess coordination number. They state that if a coordination number

3. They have asked about the CHARMM 27 force field being outdated now..How
is this true?

Please help me out in addressing the reviews. Thanks for your help in

P.S: I did not take the center-of-mass of molecular ions into account. I
dont think it is wrong for a small molecule..

Soumadwip Ghosh
Research Fellow
IITB, Mumbai

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