thank you very much sir
On Tue, Mar 10, 2015 at 7:38 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Mon, Mar 9, 2015 at 11:39 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > on a modelled system, do you think the most populated cluster will be the
> > probable one?
>
> By definition the most populated cluster is the most probable one *for
> that particular ensemble*, i.e. that doesn't mean it's the most
> probable in terms of free energy. To ascertain that you need to have
> some confidence that you are observing all relevant conformations with
> relative populations close to their Boltzmann-weighted ones (within
> the confines of whatever force field you are using), which typically
> involves multiple independent simulations run to convergence. For some
> examples of this kind of analysis see
> http://pubs.acs.org/doi/abs/10.1021/ct400862k and
> http://pubs.acs.org/doi/abs/10.1021/jp4125099.
>
> > and would increasing the number of clusters will be better.?
>
> Maybe - you will need to try a few different settings and look at your
> cluster metrics (DBI etc). There really is no way to tell beforehand
> what clustering parameters will be optimal for a given set of
> structures.
>
> Good luck,
>
> -Dan
>
> >
> > 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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> >>
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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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Mar 10 2015 - 08:30:02 PDT
