Hi,
On Mon, Dec 3, 2018 at 1:17 AM Rajbinder Kaur Virk
<rajbinderkaurvirk.gmail.com> wrote:
> I was able to perform but got two
> different types of results for two different Molecular dynamics
> simulations. In first case, the cluster with the maximum population is
> stable and in other case the population of the dominant cluster is
> decreasing with time. The DBSCAN algorithm was performed with rms
> calculated between CA,C,N.
> Attached are the two files.
> I am confused whether both the results are correct and giving some
> information or the simulations performed in the second case has to be
> looked upon again. Is there a criterion to accept or reject the simulation
> parameters on the bases of the stability of the dominant cluster?
> Please advise and thank you for your time.
These results just show that you are sampling conformations
differently in the different simulations. In the first picture you
have a system that is largely populating only a single cluster, so you
don't have much conformational variablility. In the second picture you
have multiple cluster populations increasing and decreasing relative
to each other, indicating there is much more conformational
variability. Keep in mind that unless you're doing something like
comparing cluster representatives there is no guarantee that the
structures sampled in the first simulation are similar to the ones in
the second. Something like combined clustering could be useful for
that (see e.g. the analysis done in
https://pubs.acs.org/doi/10.1021/ct400862k or
https://pubs.acs.org/doi/10.1021/jp4125099 for some concrete examples;
some sections of
http://dx.doi.org/10.33011/livecoms.1.1.5067 may also
be useful).
Also, make sure you're paying attention to your clustering metrics
(DBI, pseudo-F etc) so you can assess how well your clustering runs
are actually doing w.r.t. each other.
-Dan
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Received on Mon Dec 03 2018 - 11:30:04 PST
