thank you sir.
i am reading the paper.
sir,
one opinion please,
on a modelled system, do you think the most populated cluster will be the
probable one?
and would increasing the number of clusters will be better.?
On Mon, Mar 9, 2015 at 7:42 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Clustering tends to be more of an art form than a science, and it can
> be difficult to tell a prior what algorithm/distance metric/clustering
> parameters will give you optimal clusters. Usually something like
> hierarchical average-linkage or K-means with RMS give decent results,
> but it's not guaranteed. I highly recommend reading this article on
> clustering MD trajectories by Shao & Cheatham III et al.:
>
> http://pubs.acs.org/doi/abs/10.1021/ct700119m
>
> -Dan
>
> On Mon, Mar 9, 2015 at 12:48 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > Sir,
> >
> > I read that there are different options to perform clustering in ptraj.
> > It would be helpful if you could give some suggestions on my problem.
> >
> > I have a nucleic acid system which is a modelled one. have run a 50 ns
> > simulation (explicit).
> > obviously the starting structure may be some different from the probable
> > structure.
> > Which clustering algorithm do you think is suitable under such situation.
> >
> > thanking you
> >
> > Mary Varughese
> > _______________________________________________
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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 Mar 09 2015 - 11:00:03 PDT
