VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 29 2002 - 16:14:37 CST

Hi Marc,
  At the present time the Gromacs plugins do not read the
"BOX" simulation box data, but this could probably be altered.
I'll have to talk with my colleagues and see if we have time
to do something about this for VMD 1.8 or not. Adding a new
"simbox" graphical representation would be trivial enough, its mainly
an issue of whether we've got the necessary pieces implemented in
VMD. I know for fact that the Gromacs plugins are skipping "BOX"
records presently, so that's at least one other item that needs
correction.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 29, 2002 at 09:59:38PM +0000, Marc Baaden wrote:
>
> Hi,
>
> I have a question about the gromacs file format plugins implemented
> in VMD. As I am looking at MD data, one of the things I "like" to
> see is the simulation box. That is easy enough to do with draw
> commands, and works fine. But, right now I read the box sizes in
> separately.
>
> Now I wonder, whether the plugins in VMD read in thos extra values
> (box size) from Gromacs gro, xtc or trr files ? And if yes, which
> variable are they stored in ?
>
> If no, would it be difficuklt to implement this ?
>
> Thanks in advance,
>
> Marc Baaden 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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