VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 25 2006 - 12:39:40 CDT

Jonathan,
  Rather than writing your own trajectory writing code from scratch,
I'd suggest just using the VMD plugin interface to do this for you.
It's open source (UIUC Open Source License) and you can just put it into
your program as you wish. You could then read the code for CatDCD which
does (in part) exactly what you have in mind, and interface your code to
the plugin interface. This would allow your code to write output in any
of the trajectory formats that we have plugins for (that implement write
functionality):
  http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/

Let me know if you need more help.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jul 25, 2006 at 01:31:00PM -0400, Jonathan Ashar wrote:
> hello VMD,
>
> i am writing a molecular dynamics code as part of some undergraduate research. i'd love to be able to use VMD to visualize my results. as such, i'm trying to figure out the format of trajectory files. i'm willing to use the .dcd or .crd format, or any other format (AMBER, LAMMPS, etc.) - whatever is easiest to code.
>
> i have found this http://www.lrz-muenchen.de/~heller/ego/manual/node93.html description of the .dcd/.crd format, but i dont think i could construct a complete .dcd file from it (perhaps b/c i have no background in fortran). for example, i'm not sure what "i=1" means, or how to differentiate between different timesteps.
>
> are there any more explicit, thorough descriptions of this or any format?
> and as always, an example could be worth a hundred explanations :-P
>
> many thanks,
> jonathan ashar 

-- 
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