[gmx-developers] gromacs software development

David van der Spoel spoel at xray.bmc.uu.se
Fri Jun 29 15:08:56 CEST 2007

Carsten Kutzner wrote:
> Hi,
> I would be happy to contribute to any of the projects, especially if 
> they address
> the scaling of mdrun. In this respect the 3D FFT decomposition seems 
> most promising
> to me (apart from the fast multipole solver ;) David, could you expand a 
> bit on
> the 3d FFT topic? I guess you refer to a Daresbury/DAFT-style algorithm?

I think Erik knows a bit more about this, but he's traveling. It would 
be an algorithm that does a true 3d decomposition of the PME grid, to 
allow for using more PME nodes (right now this is limited to the number 
of grid cells in the x dimension, which means you can not use more than 
three or four times this number of nodes).
> Another question that I have is, we need an extra option in the pull 
> code which
> allows us to rotate a group of atoms around a given axis. I would now 
> start to
> implement this unless some code is already around that we could use.
I am not aware of this. Maybe Berk or Justin knows?

> Carsten
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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