[gmx-developers] XML support in GROMACS

[David van der Spoel]

On 2010-03-08 19.43, Thomas Steinke wrote:
> Dear developers,
>
> I am contacting you regarding a future XML (CML) support in GROMACS. The
> background of my question is as follows: GROMACS is one of the key
> simulation packages in the German MoSGrid project and we are involved in
> the design of data repositories using GROMACS data.
>
> On the GROMACS Developers Projects page I found that "XML-devel" for
> Preprocessing is assigned for a 4.x release and that a "XML-spec" is
> scheduled for the 5.0 release.
>
> Can somebody disclose detailed information about the status and possibly
> release dates for XML support in GROMACS?
>
> Thanks in advance,
> Thomas Steinke
>
We have long discussed this, close to eight years if memory serves me 
well, but nothing has been done in core gromacs. Some side projects of 
mine that will become part of gromacs 5.0 use libxml2 and custom-made 
XML documents. I did look into CML at the time, but the overlap with my 
needs (representing quantum chemistry data as well as experimental data) 
was not contained in CML.

There is a decision to make linking to libxml2 obligatory after gromacs 
4.1, and then a port of some gromacs files to xml might be possible. CML 
might be useful for coordinates etc., but we mainly been considering 
using XML for force fields.

We would welcome contributions of code to increase interoperability of 
gromacs. Maybe you can give some more details about your plans?

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se