[gmx-developers] MDAnalysis' libxdrfile2 vs. GROMACS' xdrfile
David van der Spoel
spoel at xray.bmc.uu.se
Tue May 12 10:32:32 CEST 2015
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?
An alternative would be to hand over he whole xdrfile library to an
A further thing to consider is whether the tng_io library should replace
the xdrfile library.
> On Tue, May 12, 2015 at 2:21 AM, Robert McGibbon <rmcgibbo at gmail.com
> <mailto:rmcgibbo at gmail.com>> wrote:
> For what it's worth, the MDTraj python package (similar to
> MDAnalysis) also includes a modified version of xdrfile, which fixes
> a few small bugs. The changes are described here:
> One of the bugs (a segfault on reading certain malformed xtc files)
> was reported to the gromacs-dev list a while ago, but nobody seemed
> On Mon, May 11, 2015 at 11:16 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
> On 2015-05-11 23:23, Dominik 'Rathann' Mierzejewski wrote:
> Dear developers,
> there seems to be a fork of GROMACS' xdrfile by the
> MDAnalysis project:
> What are the plans for xdrfile? Would you be open to
> MDAnalysis' fork changes into your library?
> They have added proper python bindings (via swig) and some
> new C APIs.
> There are also small changes in API, for example in read_trr
> parameter) and xdrstdio_(get|set)pos() functions (parameter
> I'm attaching a sanitized diff of the C code. Python changes
> are too
> extensive to make a diff of.
> The reason I'm asking is that I'm trying to package
> MDAnalysis for
> Fedora (and I became the GROMACS maintainer in Fedora
> recently as well).
> Our guidelines forbid bundling of third-party libraries - system
> versions are to be used. xdrfile is already packaged in
> Fedora, but
> MDAnalysis bundles its fork - libxdrfile2 which I have to
> and package separately. It would make everyone's life much
> easier if
> xdrfile could be simply updated to include the new python
> bindings and
> APIs so that MDAnalysis could use them.
> Are these changes compatible with the latest xdrfile changes?
> There has not been a release recently though.
> 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 <mailto:spoel at xray.bmc.uu.se>
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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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