VMD-L Mailing List

From: Vijay Vammi (vsvammi_at_iastate.edu)
Date: Fri Sep 16 2011 - 10:39:40 CDT

Hi Dr. Daniel,

Thanks for the link. I would consider it in the future.
 The reason for the temporal resolution and also for the specific protocol
is, in this work I am trying to reproduce the results from "Toward a Unified
Representation of Protein Structural Dynamics in Solution" by Markwick et
al.

The simulation is an accelerated MD simulation and would require frequent
timestamps. And I have heard from many other references about QR
factorization and want to use the technique.

Thanks
Santhosh

On Fri, Sep 16, 2011 at 10:17 AM, Hurt, Darrell (NIH/NIAID) [E] <
darrellh_at_niaid.nih.gov> wrote:

> Hi Santhosh,
>
> This may break protocol, but I find for simple clustering, it might be
> easier to use the MD Movie tool in UCSF Chimera. They have an easy-to-use
> clustering algorithm based on
> http://peds.oxfordjournals.org/content/9/11/1063 that "just works".
>
> Also, 16,000 frames for an 8 ns simulation seems like a little bit of
> overkill, unless you know that you need that kind of temporal resolution to
> build representative structures. Perhaps you could make things a little
> easier by pruning down the frames from every 500 fs to perhaps every 10 ps
> or even 100 ps to get a more manageable number of frames (800 or even 80
> frames).
>
> YMMV,
> Darrell
>
>
>
>
>
> On Sep 16, 2011, at 9:13 AM, Vijay Vammi wrote:
>
> Hello,
>
> I have a 8ns simulation with about 16000 frames. I want to cluster these
> frames to get representative structures.
>
> I want to use the QR factorization method as described in "Evolutionary
> Profiles Derived from the QR Factorization of Multiple Structural Alignments
> Gives an Economy of Information" by Patrick O’Donoghue and Zaida
> Luthey-Schulten. I see that this has been part of multiseq plugin in VMD. I
> have couple of questions regarding its use :
>
> 1). Since we are dealing with rather large number of PDB's, is it advisable
> that I run this via command line instead of GUI. I tried using the GUI but I
> see that multiseq did not load all the frames but only 2000 of them.
>
> 2). In the actual implementation the problem becomes multi-dimmensional
> because of gaps, since I dont have gaps in the structure alignment the
> problem should be reducible to traditional QR factorization. (noofCAAtoms*3
> X numframes would be the size of matrix I am trying to decompose.). Would be
> it be much faster and better if I use numpy or Matlab instead of VMD to get
> this done? Please correct me if I am wrong here.
>
> Any help or advice on this is appreciated.
>
> Thanks
> Santhosh
>
> Darrell Hurt, Ph.D.
> Section Head, Computational Biology
> Bioinformatics and Computational Biosciences Branch (BCBB)
> OCICB/OSMO/OD/NIAID/NIH
>
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