Re: [AMBER] Periodicity in MD simulations

From: Oliver Kuhn <oak.amber.googlemail.com>
Date: Wed, 20 Jul 2011 07:30:43 +0200

Hi Daniel,
thanks for the for the 'sieve' keyword explanation. Sounds reasonable.
And yes, Carlos is right, in the end, I did not pose my question right.
When I read these words "problem of periodicity", I wondered if there is a
known technical issue bringing up periodicity in MD simulations, but your
explanation asures me that there is something else meant by that, closely
related to something real.

Regarding Ignacios explanation,
I first thought of some global oscillation of the complex molecule and
looked if I can see that in the first PCA mode and I also tried clustering
high and low energy snapshots in the hope to find some hint for that but
could not find anything.

In the end I had and have the impression that it is something technical.
Yesterday I was was very surprised when I had added 10 new 'independent'
simulations to the 21 I had, and this time, these are completely
uncorrelated - and there is a technical difference, this time I had
calculated on GPUs (I used the SPDP).

At the moment, I have no more concrete question on that topic, I'm looking
closer to my data. Thank you for any help.

Regards,
Oliver

I attach one new plot with CPU simulations in "green" and GPU simulations in
"purple" (this time BOND energies).


2011/7/19 Daniel Roe <daniel.r.roe.gmail.com>

> Hi,
>
> I assume you're talking about the "cluster" command in ptraj?
>
> The "problem of periodicity" in clustering with the "sieve" keyword
> can be illustrated with this simple example. Suppose you have a
> trajectory in which you have a protein structure that has some sort of
> periodic motion to it, let's say a domain motion which provides access
> to an active site. For the purposes of this example lets say the
> "open" conformation occurs about every 10 steps, and you choose to
> cluster with a sieve of 10 - this means that on the first pass you are
> effectively clustering based on a trajectory composed of entirely
> "open" conformations, which is probably not desirable. However, if you
> sieve randomly you are probably going to get a better representation
> of the overall trajectory.
>
> Clustering experts feel free to add to this or correct me but this is
> how I understand "sieve" and periodicity.
>
> -Dan
>
> On Mon, Jul 18, 2011 at 2:17 PM, Oliver Kuhn <oak.amber.googlemail.com>
> wrote:
> > Dear Amber Users and Developers,
> >
> > I have read in the AmberTools Manual that the 'sieve' command can be set
> to
> > random to avoid THE POTENTIAL PROBLEM OF PERIODICITY.
> > What exactly is meant by that?
> > I am asking because in the course of MMPBSA calculations I have done
> several
> > 'independent' simulations using different intial random seeds.
> > Sometimes simulations are totally uncorrelated, but sometimes they are
> all
> > correlated together (for several nanoseconds). This can be seen in
> internal
> > energies, e.g. angles (attached - 21 * 2ns simulation time HIV-Protease
> drug
> > complex, blockwise averaged).
> > I have read about synchronization effects of Langevin thermostat, but
> that
> > is not what I observe. In my simulations I have the SAME starting
> structure
> > and different seeds, not different structures and same seeds.
> > I'm very puzzled about these correlations and have no idea what these
> are.
> > What I know about the nature of correlations: Either simulations are
> > correlated with pearson coefficient around 0.4 or uncorrelated with
> around
> > 0.0 and nothing inbetween.
> > My random seeds range from 01 02 and so on up to 21.
> >
> > Maybe someone can give me a hint for paper.
> >
> > Regards,
> > Oliver
> >
> > --
> > Oliver Kuhn, Department of Bioinformatics,
> > Center for Medical Biotechnology, University of Duisburg-Essen,
> > Universitätsstr. 1-5, 45141 Essen, Germany
> > phone +49 201 183-3121, oliver.kuhn.uni-due.de
> >
> > _______________________________________________
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> >
> >
>
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-- 
Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de



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Received on Tue Jul 19 2011 - 23:00:02 PDT
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