[gmx-users] g_cluster or g_clustsize

[Justin Lemkul]

On 7/29/16 1:19 AM, Seera Suryanarayana wrote:
> Dear Gromacs Users,
>
> I would like to do clustering of my trajectories. When I look into gromacs
> tool for clustering, I got g_cluster which is based on the RMSD and the
> other one is g_clustsize which computes the size distributions of
> molecular/atomic clusters in the gas phase. Mine is protein in solvent
> system. Here I got confusion whether I use the g_clustsize. Which one I
> have to use, either g_cluster or g_clustsize? Kindly suggest me.
>

Use g_cluster.  g_clustsize is for computing e.g. the aggregation of multiple 
molecules.  If you have one protein, your cluster size is always one since 
there's really nothing to compute.

-Justin

-- 
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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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