VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Jan 06 2010 - 15:58:02 CST

Thank you all for the answers.

I am not using stride or writing every other frame, because I want to
visually look at the entire trajectory at once. So, it seems that if I want
to look at the entire trajectory at once, I will need to upgrade the memory?

When I start up VMD, typically more than 3 GB of memory is available, and
indeed, there is a lot of swapping going on when the frames are loaded.

I will follow up with more updates tomorrow (trying 1500 frames only, and an
exact calculation of how much memory is available before and after running)

-Maria

On Wed, Jan 6, 2010 at 6:09 PM, Irene Newhouse <einew_at_hotmail.com> wrote:

> I have a linux box myself with 4GB of memory. It can handle ~1.2GB of
> trajectory, but not much more. Be sure you don't have a lot of other stuff
> running when you process it. I would also recommend updating to 1.8.7. You
> have 2 options for very large trajectories: either use catdcd & the
> stride option to extract every other time step [or whatever you need to get
> the file size down] or use bigdcd and scripting to process. bigdcd processes
> a frame at a time, rather than loading the entire file at once. It's loading
> the entire file at once that creates the problems. I haven't done the
> scripting thing myself; so far, I've only used the stride option.
>
> Irene Newhouse
>
> ------------------------------
> Date: Wed, 6 Jan 2010 11:32:30 +0100
> Subject: vmd-l: VMD hangs up with a file size ~ 1.2 GB ?
> From: mariagoranovic_at_gmail.com
> To: vmd-l_at_ks.uiuc.edu
>
>
> Hi,
>
> I am using VMD v. 1.8.6 to load up a trajectory of ~ 1.2 GB on the VMD GUI
> on my linux box which has 4GB memory, and a 512 MB Nvidia card. VMD hangs
> up, and freezes the entire system. Any ideas why this should happen ? VMD
> also slows down considerably when I load up such large files. Any ideas or
> solutions?
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>
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-- 
Maria G.
Technical University of Denmark
Copenhagen