Re: [AMBER] cpptraj error

From: Rajbinder Kaur Virk <>
Date: Tue, 4 Dec 2018 14:48:29 +0530

Hello sir

I am grateful for your response, I shall follow the papers you suggested.

Thank You

With Regards
Rajbinder Kaur Virk

On Tue, Dec 4, 2018 at 12:54 AM Daniel Roe <> wrote:

> Hi,
> On Mon, Dec 3, 2018 at 1:17 AM Rajbinder Kaur Virk
> <> 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
> or
> for some concrete examples;
> some sections of 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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*With regards*
*Rajbinder Kaur Virk*
*Research Scholar *
*Department of Biophysics*
*Panjab University *
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Received on Tue Dec 04 2018 - 01:30:02 PST
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