[gmx-developers] XML support in GROMACS
David van der Spoel
spoel at xray.bmc.uu.se
Mon Mar 8 20:06:59 CET 2010
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
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