[gmx-users] regarding g_rdf

Justin Lemkul jalemkul at vt.edu
Wed Nov 26 04:28:52 CET 2014

On 11/25/14 11:44 AM, soumadwip ghosh wrote:
> Dear all,
>                I am willing to calculate the rdf of certain cations from
> different group of molecules in the system. For example, I have got a DNA
> backbone (having P, O1P and O2P atoms), DNA major groove (having all the
> atoms a guanine and cytosine residue can have together) and a minor groove
> (having all the atoms an adenine and thymine residue can have together).
> Now I want to calculate g_rdf between Na/ backbone, Na/minor and Na/major.
> Should I proceed with the -com option or not? I am not understanding the
> concept of -rdf option for selecting between geometry/molecules.

I would not use -com in this case, given the level of detail you're likely to 
need when doing this analysis.  It's not useful to get an RDF of ions around a 
COM of some residues in such a specific location, especially when binding to 
specific moieties may be of particular interest.



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


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