[gmx-users] small molecule aggregation analysis

Justin Lemkul jalemkul at vt.edu
Tue May 24 18:35:06 CEST 2016

On 5/24/16 12:19 PM, Surahit Chewle wrote:
> Hello Everyone,
> I have simulated a system of 10 synthetic drug molecules (each 20 atoms) in
> small organic solvent, methanol on Gromacs 4.6.5
> as far as I have read, there are many tools available for protein
> aggregation, but if you can suggest a tool of choice for small molecule
> aggregation, for ex, radial distribution function that will be helpful.
> Fairly new to Gromacs and this is my first post, so kindly be gentle if I
> have made a mistake posting this message.

I don't think there's necessarily any tool that is predisposed to being intended 
for protein aggregation; most of the analyses applied in those cases are rather 
generic - contacts, distance matrices, buried SASA, possibly RDF, etc.



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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