VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 06 2006 - 18:08:01 CST

Hi,
  So you're loading the XYZ file on VMD in a Suse Linux running on a
32-bit x86 processor? When you load the trajectory, are you attempting
to load the whole thing, or only part of it? It's also possible you are
running out of memory on your PC, how much RAM does the machine have?
One way to determine if it's a file size issue or a RAM issue is to tell
VMD to start reading frames at frame 10,000 and see if that fails immediately
or if it reads 5,000 or so frames (as before) and then quits. If it fails
immediately, then it's probably a file size or filesystem issue, if it
runs for 5,000 then stops it may be a RAM issue.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 06, 2006 at 09:55:20PM +0100, bizoniusz_at_o2.pl wrote:
> Dear Mr. Stone!
>
> My trajectory is in XYZ cpmd format, 7 columns, the first one is the number of steps, next x y z and the last three are velocities. For CPMD calculation I used Itanium64 processor and Rocks Linux. I have new VMD 1.8.410b and I use it on Suse Linux distribution on PC. The trajetory files is a very big. Its size is about 2GB.
> Thaks for your help.
>
> Best regards!
>
> 

-- 
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