VMD-L Mailing List

From: Peng Tao (ptao_at_chemistry.ohio-state.edu)
Date: Wed Sep 10 2003 - 15:12:44 CDT

Dear John Stone,

Thank your replying.

Here are the details:
////////////////////////////////////////////////////////////////////////////
//////
Microsoft Windows 2000 [Version 5.00.2195]
vmd > vmd
Info) VMD for WIN32, version 1.8.1ss03 (May 27, 2003)
Info) OpenGL renderer: GDI Generic
Info) Features: STENCIL
Info) Textures: 2-D (1024x1024)
Info) Spaceball driver not installed. Spaceball interface disabled.
Info) No joysticks found. Joystick interface disabled.
Found 69 plugins or data handlers in directory
        'C:/Program Files/University of Illinois/VMD/plugins/WIN32/molfile'.
////////////////////////////////////////////////////////////////////////////
//////

The traj file is mdcrd file from the AMBER7 MD simulation. The actual length
is 2,147,483,647 byte. The system I am simulating contains 32901 atoms.

Yes I am using 32-bit computer, but I didn't try to read in the whole
trajectory file. But VMD couldn't access any frame after 2684. Do you think
it is due to 32-bit addressing limit?

Is there any way for me to divide the large mdcrd file into parts? Therefore
I can avoid such limit?

Thank you very much.

Yours Sincerely,
Peng Tao

Chemistry Department
The Ohio State University

----- Original Message -----
From: "John Stone" <johns_at_ks.uiuc.edu>
To: "Peng Tao" <ptao_at_chemistry.ohio-state.edu>
Cc: <vmd-l_at_ks.uiuc.edu>; <vmd_at_ks.uiuc.edu>
Sent: Wednesday, September 10, 2003 3:56 PM
Subject: Re: Reading large traj file error or how to divide a large traj
file into parts?

>
> 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
> 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
>