VMD-L Mailing List

From: Vijay Vammi (vsvammi_at_iastate.edu)
Date: Fri Sep 16 2011 - 15:42:45 CDT

Hi John,

Thanks for looking into it.

But I am still interested to know if any one has done this before and assert
if I am right when I say the problem reduces to two-dimmensional QR
factorization when dealing with MD trajectories.
I am writing a numpy code for it and would check with existing
implementation on a smaller dataset.

Thanks
Santhosh

On Fri, Sep 16, 2011 at 3:02 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Hi,
> It sounds to me like whichever GUI is being used is causing VMD to
> load all of the files concurrently, and that the host operating system
> is running out of open file handles. If the file loading is done through
> multiseq, then it may be that we need to add a "waitfor all" to the
> code that causes the list of files to be loaded. I'll talk to Kirby
> about this and see what we come up with.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Sep 16, 2011 at 02:52:47PM -0500, Vijay Vammi wrote:
> > Hi Kirby,
> >
> > I am writing the code in numpy for QR factorization. Since I dont have
> any
> > gaps in my alignment the problem reduces to simple QR factorization.
> >
> > But to answer your question :
> > I get this error message : "couldn't read directory "/usr/tmp/": too
> > many open files" after 1092 files. And this makes me use only 1092
> files.
> >
> > I am loading using GUI, select all the files from import data. I do
> have
> > the latest version.
> >
> > Thanks,
> > Santhosh
> >
> > On Fri, Sep 16, 2011 at 2:22 PM, Kirby Vandivort <kvandivo_at_gmail.com>
> > wrote:
> >
> > Santhosh,
> >
> > We have successfully loaded about 100,000 sequences into the version
> of
> > MultiSeq that is being distributed with VMD 1.9 (are you using the
> > latest version?), so I want to make sure that everything is working
> as
> > it should.
> >
> > How are you attempting to load the 16,000 frames?
> >
> > Thanks,
> >
> > Kirby
> >
> > On Fri, Sep 16, 2011 at 8:13 AM, Vijay Vammi <vsvammi_at_iastate.edu>
> > 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
> >
> > --
> >
> > Kirby Vandivort
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
>