VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 17 2007 - 12:59:16 CST

Hi,
  If you're loading 20,000 frames, you'll need this much
available memory to load the trajectory:
  20000 frames * 12 bytes per atom * numatoms

So, if you have 100,000 atoms and 20,000 frames, you'd need:
  20000 * 12 * 100000 = 24 gigabytes of memory

If you had 10,000 atoms, then you'd only need 2.4GB of memory.

If you don't want to do the math, another way to evaluate the amount
of physical memory you'll need with the current versions of VMD is
to look at the size of the DCD file itself, which is basically the
same as the math above (unless you have fixed atoms).

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 17, 2007 at 01:50:07PM -0500, Vishal Kopardé wrote:
> Hi All,
> I have 20000 frames in my dcd file and while opening it with a step
> of 1 VMD quits after loading ~4100 frames. But if I load with a step
> of 10 then it does load the 2000 frames. Is this due to memory
> restrictions? Is there a way around it?
> Regards,
> Vishal
>
>
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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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