VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 18 2010 - 10:00:08 CDT

Hi,
  At the present time, there's not a way to rapidly "fast forward"
to an arbitrary frame of an XTC file in VMD, the time it's currently
taking is due to the need for the current version of the XTC reader
plugin to parse its way through the trajectory up to the starting
frame you have specified.

I didn't personally write the gromacs plugins
in VMD, so I'll have to investigate whether it will be possible to
improve this behavior in a future version.

For the time being I would recommend chopping your trajectories into
smaller chunks to make it easier to process frames near the end of
the trajectory.

I don't know if Gromacs provides tools for this or not, but I would
expect that Gromacs might have the best tools for splitting or
concatenating the XTC files efficiently. Once split, you could then
work with them for efficiently in VMD from then on, particularly if
you're accessing only the last parts of a trajectory and not processing
the entire thing.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 18, 2010 at 11:44:56AM -0300, Alberto Sergio Garay wrote:
> Dear all
>
> I have made a tcl/tk script for vmd, which runs in text mode. My
> script needs to load just the last part of a big trajectory xtc file,
> but I takes a lot of time to do it. Is there any way to improve this
> loading procedure?
>
> I've used the following lines in my script:
>
> mol new file.gro waitfor all
> mol addfile file.xtc type xtc first 40000 last 60000 - step 1 waitfor all
>
> Thank you in advance.
>
> Sergio
>
>
> --
> Dr. Sergio Garay
> Facultad de Bioquimica y Cs. Biológicas
> Universidad Nacional del Litoral
> Santa Fe - Argentina
> C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
> Argentina
> Ph. +54 (342) 4575-213
> Fax. +54 (342) 4575-221
>
>
>
>
> 

-- 
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