VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 16 2006 - 17:12:32 CDT

Rima,
  You can either use the "first", "last", and "stride" controls in the
molecule file browser window, or use the same options with the mol new/addfile
text commands. If you want to see the whole trajectory, I'd recommend just
setting the "stride" value in the GUI to something like 10, as that will
cut your memory use down to 300MB rather than 3GB. I hope to make changes
in future versions of VMD which will warn the user to help prevent them from
loading trajectories that are too large to fit in available memory.
In the mean time, just set the stride/step size (GUI / text command) and
see if that does what you need.

  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Apr 16, 2006 at 02:01:52PM -0700, Rima Chaudhuri wrote:
> Hello!
> I have a 3GB DCD file at this moment, the frames were written at every 100 steps, the simulation is still running and is only 40% complete (of total 1ns). As of now it has some 4000+ frames. The huge DCD file cannot be uploaded in VMD, it reaches its memory limit and crashes. Is there a way I can break the DCD file into sub-parts and then upload it? or if there is any way around this problem?? Any help would be much appreciated.
>
> Thanks
> -Rima.
>
>
> "I can tell you fancy, I can tell you plain, you give something up for everything you gain. Since every pleasure's got an edge of pain. Pay for your ticket and don't complain" - Bob Dylan
>
> ---------------------------------
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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