[gmx-developers] Patch for 3DC for non-neutral systems but parallelization still has to be done

David van der Spoel spoel at xray.bmc.uu.se
Wed Sep 28 11:18:03 CEST 2016

On 27/09/16 21:10, Philip Loche wrote:
> Dear all,
> we created a patch for gromacs 5.1 to correct the forces and the potential for charged systems using the EW3DC method. The equations are implemented according to
> Ballenegger et. al (http://dx.doi.org/10.1063/1.3216473). (29) for the potential and (30) for the force. We reproduced their results (section IV A and B). You can of course get the input files. The patch can be found on github:
> https://github.com/PicoCentauri/gromacs/commit/0f9438494281668e0f9282765009889c209cb10f
> The code works fine for a single thread but unfortunetaly fails for several. The problem is the summation over the atoms in line 535, where only the ones in the master process are included but not all. Unfortunately I’m not able to fix this.
> I also wanted to create a feature request on redmine, but currently it is not possible to register. It would be very nice if someone can help with the implementation.
> Thank you and best regards,
> Philip
Thanks for contributing to gromacs. First, a change like this can only 
be incorporated in the master branch, so please try to reimplement it in 
the master branch. Second please just upload it to gerrit.gromacs.org by 
making an account there.

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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