VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 11 2006 - 16:23:26 CST

Kim,
  You can split large DCD files like this using CatDCD, which will preserve
the DCD header on the various smaller files you can create with it.
I've just updated the CatDCD page with newly built executables with
the most recent software:
  http://www.ks.uiuc.edu/Development/MDTools/catdcd/

Give CatDCD 4.0 a try and let us know if you need more help.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 11, 2006 at 11:41:49AM -0800, Kim Gunnerson wrote:
> Hi John,
>
> I am running VMD on a Windows XP platform and also having trouble reading large files. The dcd file is larger than 2 GB similar to how others have been. When I try to load them I get the following error messages:
>
> Error message in VMD window:
>
> Unable to read molecule
>
> Error message in dos prompt window :
>
> DCD file (filename) appears to contain no time steps
> Could not read file (filename)
>
> I get the same messages if I try to use the First, Last, and Stride as I have read others have done to break up their large files.
>
> I am running NAMD on a cluster using Linux and then transfering the files to my desktop computer to analyze. In an attempt to at least get some of the trajectory I have used the split command to break up the file on the Linux system and then download them to the desktop. I can load the first part into VMD without any difficulties if the file is smaller than 2GB. The other parts I am unable to load...I figured it is because there is necessary information at the beginning of the binary file that VMD needs and because I am splitting by size not looking for a particular step.
>
> This implies to me that there are proper time steps (I see evidence of this in the output log file containing the energy information) but that once the file gets a certain size VMD can't open it.
>
> Any advice you might have to help me would be greatly appreciated. Presently, I am doing a workaround where I run the MD for a shorter period of time and then do re-starts...Not exactly an elegant solution.
>
> Thanks
> Kim
>
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
> Kim Gunnerson
> Office: Bagley 311
> Prezhdo Research Group
> GK-12 Project Manager
> gunnek_at_u.washington.edu
>
> "No one can make you feel inferior
> without your consent."
> Eleanor Roosevelt
> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 

-- 
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