[gmx-users] Regarding RDF calculations

[Justin Lemkul]

On 2/27/15 2:00 AM, soumadwip ghosh wrote:
> 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?
>

Dealing with RDFs or occupancies around DNA is extremely challenging.  Normal 
RDF lack sensitivity and do not fully describe the behavior of ions around DNA, 
especially given the asymmetry between major and minor grooves.  See, for 
instance, dx.doi.org/10.1021/ja0629460

> 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 They have asked about the CHARMM 27 force field being outdated now..How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?
>

Yes.  There are specific improvements in CHARMM36 for DNA and RNA, with a 
reparametrization of some important backbone torsions in DNA that have 
implications for sampling substates of B-DNA and correct sugar puckering.

-Justin

> Please help me out in addressing the reviews. Thanks for your help in
> advance.
>
> 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..
>
>
> Regards
> Soumadwip Ghosh
> Research Fellow
> IITB, Mumbai
> India
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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