[gmx-users] Major code reorganization in git coming up

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Jan 1 12:59:54 CET 2011

Hi Erik,

Happy New Year!

Last year (:p) I rewrote the routine from Andrea Amadei for
application of rotational constraints in a statistical mechanical
consistent manner. It's completely parallellelellized and consistent
with pd/dd as well as application every so many steps. The tests seem
good, although some small changes in handling the reference structure
may be required. Bottom line is, it was a pain getting it working with
the >4.1 releases due to all the changes and I'm a bit afraid of
what's to come :) So maybe a good idea to add it soon for beta? I can
provide the patch against the release-4.5-patches. I've implemented it
as an additional COMM removal mode.



On Thu, Dec 30, 2010 at 7:09 PM, Erik Lindahl <erik at kth.se> wrote:
> Hi!
> We figured we'd celebrate the upcoming new year with some major changes in the git development branch, consisting primarily of C++ support and a more modular organization of files.
> This is a gradual process, so this mail is a bit of a warning-message that the master/development branch might have some issues with compilers/build environments the next couple of weeks.
> If you occasionally use a git build to run production simulation, just use the release-4-5-patches branch instead, and everything should be fine.
> However, If you are working on your own code based on the git master branch, it might be a good idea to either switch to the release-4-5-patches branch, or create your own branch that you no longer sync with master as frequently. In the latter case you might have to go through some pain to port your code back to the new file organization later (sorry about that).
> The upside of all this is that the file organization will gradually get easier to understand, and the code itself should also get much more modular and readable (which we hope will lead to a faster release schedule and more features :-)
> Happy new year!
> Erik
> --
> Erik Lindahl <erik at kth.se>
> Professor of Theoretical & Computational Biophysics
> Department of Theoretical Physics & Swedish e-Science Research Center
> Royal Institute of Technology, Stockholm, Sweden
> Tel: +46855378029 Cell: +46703844534
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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