VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Sep 15 2005 - 11:07:50 CDT

Hi,
  Most of us did this by reverse engineering and or reading source code.
I've already forgotten where we got the specs for the cell size records,
but you should feel free to read the VMD DCD code if you like. I've attached
the DCD reader/writer plugin from VMD. You'll be interested in the
read_charmm_extrablock() function, as that's where our code for reading
the unit cell info exists. It's simple, just a block of 6 double precision
numbers. The tricky part is that you also have to setup the DCD header
correctly (emitting a '1' rather than a '0' in one of the header records)
to indicate that the file contains cell info. This is shown on line 619 of
our DCD writer code. Hopefully you can make sense of this. Please find
the dcdplugin.c file attached to this email.

  John Stone
  vmd_at_ks.uiuc.edu
 

On Wed, Sep 14, 2005 at 04:09:06PM +0200, Tatyana Kuznetsova wrote:
> Dear vmd-l,
>
> We use our home-grown Fortran package to do molecular dynamics and VMD
> to visualize the results. I would like to add the MD cell size
> information to the dcd files, but can't find any sites that outline the
> new dcd format. Can anybody point out *any* site describing the dcd
> format fields.
>
> Thanks in advance.
>
> Dr. Tatyana Kuznetsova
> Institute of Physics and Technology
> University of Bergen
> Bergen
> Norway 

-- 
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