VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 09 2006 - 10:33:27 CST

Lily,
  How much memory does your computer have? You may have to use the 'stride'
option in the file loading menu when loading your trajectory to skip frames
so you don't run your machine out of memory. In order to load the 300K atom
system with 400 frames, you'll need _at least_ 1.5GB of RAM on your machine.
Ideally, you'd have about 2GB of RAM in order to load the entire trajectory,
since some of your memory will be used by Windows XP itself, and by any
other software you're running. If you don't have 2GB of RAM, then you'll need
to reduce the number of timesteps you read from your trajectory, either by
decreasing the total number with the first/last options, or by increasing the
stride parameter to reduce the fraction of loaded frames to a level that your
machine can handle. One simple way to calculate this for your specific case
would be to divide 2GB (the ideal amount of memory) by the amount of RAM
you actually have (say 512MB) and use that as the 'stride' value, which in
this example case would be 4.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 09, 2006 at 08:22:57AM -0800, lily jin wrote:
> I run VMD1.8.3 on windowXP and I have met this probrom:
> "winvmd has encountered a problem and needs to close. We are sorry for the inconvenience."
>
> A few weeks ago, this happened when I change the drawing method into bonds from line or ribbon. Our IT technician solved the problem after intalling NVIDIA driver.
> Now, this error message come again when I try to open my trajectory file. The The protein has 51000 atoms and it is in water box. Totally there are 308062atoms. And the dcd file has 400 frames. The error message comes out when it gose to 386 frames.
>
> Have you ever met this problem? What might be the cause? Thank you very much!
>
>
>
> Lily
>
> ---------------------------------
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-- 
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