VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 10 2003 - 14:56:18 CDT

Hi,
  You've just discovered the 32-bit addressing limit. :-)
Unless you're using a 64-bit computer (i.e. Sun, SGI, IBM RS/6000,
Itanium, or Opteron / Athlon64) you are not going to be able to easily
load files that are larger than 2GB. You didn't mention which version
of VMD you're using nor which platform you're running on, but it definitely
sounds to me like you're running on a 32-bit machine (or at least a 32-bit
version of VMD).

If you have a 64-bit Sun, SGI, etc sitting around in your lab, that's
going to be the easiest way for you to load the large file. We have
64-bit LFS code in some of the VMD file reader plugins, but I don't
think that this has made it into our Gromacs readers quite yet.
(I assume that "traj" in this case refers to a Gromacs .trj file?)

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 10, 2003 at 03:01:22PM -0400, Peng Tao wrote:
> Dear VMD users,
>
> After 2ns simulation (nstlim=2,000,000, ntwx=200, so there should be 10,000 frames in the traj file ), the file size is about 2GB. It's so large that I couldn't read it in for one time. So I tried to use VMD to read in 1000 frames each time and analyze the results, that is, read 0-999 frames, deleted them, then read 1000-1999 frames, etc..
>
> But for 2000-2999 frames VMD stopped at 684. After deleting the read frames (2000-2684), I tried to read 2685-2999 frames, but got nothing.
>
> Then I tried to read one frame from every 10 frames, that is, for Frames: First=0, Last=-1, Stride=10. After long time waiting, I only got 269 frames. It seems to me that VMD only can access the frist 2685 frames of this large traj file.
>
> Is there any way to access other frames? Or can I cud the large traj file into parts, therefore I can access the frames those are near to the end?
>
> Thank you very much.
>
> Have a nice day and happy Moon Festival.
>
> Yours Sincerely,
> Peng Tao
>
> Chemistry Department
> The Ohio State University
> 

-- 
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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