VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 21 2005 - 11:30:01 CST

Philip,
  I assume you're using one of the most recent versions of NAMD,
in which case it ought to be saving the periodic cell size in
the resulting DCD trajectory files. If you set the NAMD config
options correctly, you won't have to do anything manually to get
the periodic cell info into VMD, it'll just load from the DCD file.
If you have questions about setting your NAMD options correctly, you
can email namd-l_at_ks.uiuc.edu and they should be able to help you.

If it turns out that your DCD trajectories don't contain periodic
cell information, then it's not too difficult to read in an XST
file, the main issue is that you'll have to match up the DCD frames
with the correct XST data. I believe Jan Saam's PBCWrap script
includes code for reading the XST files.

Let us know if you need more help.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Feb 21, 2005 at 09:49:51AM -0700, Philip Blood wrote:
> Hi,
>
> I am reading in frames from a dcd file for a simulation with changing
> box size. For each frame I would like to display some of the periodic
> images. I am wondering if there is a slick way to do this without
> having to type in "molinfo 0 set a ..." for each frame. So I guess I
> would need a script that advances the frames and then reads the cell
> value from my NAMD xst file and then sets the cell dimension using
> molinfo. Has anyone ever tried this? I am not very familiar with all
> the commands or the scripting interface, so any tips would be appreciated.
>
> Thanks,
> Phil Blood 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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