[gmx-developers] MDAnalysis' libxdrfile2 vs. GROMACS' xdrfile

[Mark Abraham]

Hi,

Yes, but first we think we need at least one non-GROMACS viewer to support
it (Magnus Lundborg has been working on it with VMD, see his post earlier
in this thread), so that us defaulting to TNG output is reasonable. We
probably need to re-implement some of the eigensystem-based tools that
abuse .trr before we can retire it, too. I'm certainly keen to move a lot
of the extraneous mdrun output (pulling, replica exchange, fancy FE
methods) into the TNG file, and hopefully energies too.

Mark

On Fri, Oct 16, 2015 at 10:31 AM David van der Spoel <spoel at xray.bmc.uu.se>
wrote:

> On 14/10/15 15:33, Mark Abraham wrote:
> > Hi,
> >
> > There is
> >
> > git clone git://git.gromacs.org/libxdrfile.git
> > <http://git.gromacs.org/libxdrfile.git>
> >
> > but whoever's been making updates (David?) hasn't pushed whatever
> > content has gone into 1.1.[234]
> Isn't all of this becoming obsolete due to the tng library?
>
> >
> > Mark
> >
> > On Wed, Oct 14, 2015 at 2:51 PM Dominik 'Rathann' Mierzejewski
> > <dominik at greysector.net <mailto:dominik at greysector.net>> wrote:
> >
> >     On Tuesday, 12 May 2015 at 10:19, David van der Spoel wrote:
> >      > On 2015-05-12 08:27, Roland Schulz wrote:
> >      > >Should we add xdrfile to gerrit so that we can easily accepts
> >     patches
> >      > >our standard way?
> >      > Would be great if it is not too much work...
> >
> >     Sorry to revive an old thread, but it looks like there was no
> >     conclusion. Where is the source code for xdrfile located? I can find
> no
> >     other location than
> >     http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
> >     which links to
> ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
> >
> >     In the meantime, there is ongoing work to rewrite xdrfile by
> MDAnalysis:
> >     https://github.com/MDAnalysis/mdanalysis/issues/419
> >
> >     I mentioned this thread there. Could you guys join efforts to avoid
> >     duplication of work?
> >
> >     Regards,
> >     Dominik (still working on packaging MDAnalysis for Fedora)
> >     --
> >     Fedora http://fedoraproject.org/wiki/User:Rathann
> >     RPMFusion http://rpmfusion.org
> >     "Faith manages."
> >              -- Delenn to Lennier in Babylon 5:"Confessions and
> >     Lamentations"
> >     --
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>
> --
> 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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