VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 07 2005 - 16:14:26 CDT

If you're analyzing multi-gigabyte trajectories, it's definitely
a good plan to run VMD where the trajectories are rather than trying
to access them remotely or to copy them to a local machine, if you don't
have a need to visualize them. If you do need to visualize them, you
can save a lot of time and energy by using VMD or CatDCD to make a
smaller trajectory that skips frames, that way you're only downloading
a fraction of the whole thing.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 07, 2005 at 12:54:00PM -0400, Jindal Shah wrote:
> Thanks for the suggestions. This seems to work. Downloading the files
> from the remote machine is difficulty given the size of the trajectory files
> ~few gigabytes
>
> Jindal
>
> On 9/7/05, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> > Hi,
> > There's no built-in way for VMD to access remote files other than
> > structures that reside in the main PDB repository. If these files can
> > be downloaded via HTTP, it would be relatively simple to write a Tcl
> > script
> > that does this however. Yes, you can run VMD with no graphics. Just
> > execute VMD with this command:
> > vmd -dispdev text
> >
> > If you want to run VMD in a batch mode, you can do that as well by
> > redirecting stdin/stdout and running it in the background. These startup
> > commands are documented in the VMD User's Guide.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Sep 07, 2005 at 12:25:50PM -0400, Jindal Shah wrote:
> > > Hello,
> > >
> > > I was wondering if I can analyze the pdb files that are stored on a
> > remote
> > > machine
> > > but using VMD installed locally. When I try to open the VMD display, it
> > > returns with
> > > an error that X server does not support OpenGL extension. Also, is there
> > a
> > > way to run
> > > VMD without opening the display , i.e. in a text mode?
> > >
> > > Thank you,
> > > Jindal
> >
> > --
> > 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
> > 

-- 
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