Thanks Daniel, it was helpful.
On Mon, May 11, 2015 at 9:09 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Mon, May 4, 2015 at 10:35 AM, newamber list <newamberlist.gmail.com>
> wrote:
> > Another way someone suggested me is Clustering analysis. As far as I
> > googled this term, one gets few clusters and one can choose lowest RMSD
> > structure from centroid of most populated cluster. I am just wondering
> > would this be a good way of choosing best representing structure?
>
> Representative structures (which have lowest cumulative distance to
> all frames in a cluster) are already output by the
> 'repout'/'singlerepout' keywords. Centroids are not written, but you
> can think of average structures as the centroid where coordinate
> metrics are concerned.
>
> > Also cpptraj manual suggests there are two algorithms to choose. Which
> one
> > I should use in my case. Also, when someone says 'distance from centroid'
> > does it usually means RMSD? I am confused with terminologies used.
>
> There are actually 3 clustering algorithms in cpptraj now: kmeans,
> hieragglo, and dbscan. In the context of clustering, the distance
> metric is RMSD by default - if you choose something else (like 'data')
> then the distance refers to that.
>
> -Dan
>
> >
> > Thanks for any help.
> > Jiom
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>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Mon May 11 2015 - 14:00:04 PDT
