VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 16 2011 - 15:02:59 CDT

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
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