[gmx-users] RDF calculation.

[Marcelo Depólo]

Well, since you are not interested in the duplex stability, I would not use
-COM. See, during the simulation, the center-of-mass of such a small helix
part can drastically move, leading to a questionable result. Check your
system and make sure that you will not face this situation.

About the PMF, that depends on the ions you are using and the forcefields.
It is already known that some of them are poorly described, so check that
out too.

Hope it can help!
Cheers!

2014-12-27 7:17 GMT-02:00 soumadwip ghosh <soumadwipghosh at gmail.com>:

> 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
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-- 
Marcelo Depólo Polêto
Biochemicist
University of Viçosa - Brazil