VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 27 2006 - 15:28:31 CST

Hi,
  I've just posted a new test version of VMD 1.8.4 which includes
a DCD plugin that should correctly read/write files larger than
2GB, even on 32-bit CPUs, through the use of native Windows I/O calls.
The other platforms should remain the same. The new beta 10
test version is available here:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Enjoy,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 25, 2006 at 11:33:19PM -0800, Vineet Pande wrote:
> Thanks John-
> I am running on Windows XP, trajectory is a merged and
> recentered CHARMM output with 2000 frames which i
> think is making the problem; because when I load the
> same trajectory but with less frames (i.e. around 20
> frames by jumping more picoseconds of trajectory per
> frame), it works fine. So its either the "file size
> problem" or as you mention the "platform problem". Do
> we expect to load very many frames with solvent for a
> large system like mine in any other platform like
> Linux etc.? I am dealing with a system of total 107295
> ATOMS and the trajectory is a .cor (binary) CHARMM
> file, which is read correctly as a "CHARMM; NAMD;
> XPLOR, DCD" type in VMD.
>
> Regards..
> Vineet Pande
> Karolinska Institute, Stockholm
>
>
> --- John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Hi,
> > What file format is your CHARMM trajectory written
> > in?
> > Is it being loaded by VMD as a DCD file, or some
> > other format (COOR?)?
> > If it is a DCD file, the next question is what
> > platform you're
> > running VMD on? The specific error message you
> > mention below
> > doesn't sound like anything in the DCD reader, thus
> > my initial
> > question about which file format your trajectory was
> > written in.
> > If the trajectory is written as a COOR file (read in
> > VMD by corplugin),
> > then the problem could be one of several things. I
> > just fixed a couple
> > of bugs in corplugin, specifically affecting the
> > extended COOR format
> > for structures with more than 99,999 atoms. It
> > could be that you've
> > just run into one of the problems I recently fixed.
> > The next test version
> > I post on the web site will include the new
> > corplugin, and may fix your
> > problem if it's an issue with file formatting. If
> > your problem is due
> > to the file size, then the solution will depend on
> > which platform you're
> > running VMD on.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Jan 25, 2006 at 04:21:53AM -0800, Vineet
> > Pande wrote:
> > > Hi,
> > > I am trying to load a CHARMM trajectory (after
> > merging
> > > smaller chunks and recentering solvent), but VMD
> > > (version 1.8.4b6) gives an error message saying-
> > Error
> > > opening file: improperly formatted line. The
> > number of
> > > atoms in my system are 107295 and the size of the
> > PBC
> > > trajectory is around 2GB. When I load similar file
> > > without solvent and PBCs, it works fine. Does it
> > have
> > > anthing to do with size limits?
> > >
> > > Thanks in advance,
> > > Vineet Pande
> > > Karolinska Institute, Stockholm
> > >
> > >
> > > __________________________________________________
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> > --
> > NIH Resource for Macromolecular Modeling and
> > Bioinformatics
> > Beckman Institute for Advanced Science and
> > Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana,
> > IL 61801
> > Email: johns_at_ks.uiuc.edu Phone:
> > 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax:
> > 217-244-6078
> >
>
>
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078