From: Jindal Shah (jindal.shah_at_gmail.com)
Date: Wed Sep 07 2005 - 20:09:32 CDT

John,
 That is what I did. I could run VMD in the batch mode command
vmd -dispdev text -eofexit <*.tcl> output.log
and analyze the
large trajectory files on the remote machine. Thank you for the CatDCD
information.
 Jindal

 On 9/7/05, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> 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
>