[gmx-users] RDF calculation.

[Justin Lemkul]

On 12/27/14 4:17 AM, soumadwip ghosh wrote:
> 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?
>

I'm not sure it's useful.  Choline is a rather flexible molecule, so simply 
considering the COM of the minor groove vs. all atoms of choline is probably 
going to give you a very noisy profile.

> 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?
>

This doesn't generally work well for ions, but the quality depends on the force 
field.  Depending on what the ion is, the exchange rate may be impossible to 
observe in an atomistic simulation.  The exchange rates for most common ions can 
range from nanosecond (feasible with MD) to microsecond (not reasonable, even if 
the force field is very accurate).

-Justin

> 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
>

-- 
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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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