From: Axel Kohlmeyer (akohlmey_at_vitae.cmm.upenn.edu)
Date: Thu Jan 26 2006 - 07:09:22 CST

On Wed, 25 Jan 2006, Vineet Pande wrote:

VP> Thanks John-
VP> I am running on Windows XP, trajectory is a merged and

while VMD itself is only limited by the available memory,
the i/o interface of windows imposes a 2GB filesize
limit. if you split your trajectories into smaller
chunks, it should work.

btw.: this _has_ been discussed here _numerous_ times.
john, perhaps it would make sense to document it in
the manual in the sections mentioning reading files
(via GUI or script).

regards,
   axel.

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

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.