[gmx-developers] distance restraints and domain decomposition
ckutzne at gwdg.de
Fri Jun 8 08:41:21 CEST 2018
> On 8. Jun 2018, at 07:52, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> Den 2018-06-07 kl. 16:33, skrev Bert de Groot:
>> On 06/07/18 16:22, Berk Hess wrote:
>>> If you are sure the x, y and z components are shorter than half the box diagonal, your results should be fine.
>> so far, so good. The involved distances behave as expected based on the restraint input in the simulations thus far so the restraints seem to be doing what they should.
>>> If you think such a setup is important to run efficiently in parallel, we can think of ways to make this work.
>> thanks. Right now I cannot judge how frequently we'll need a setup like this in the future. For the current set it appears we'll be able to get decent throughput on available openMP nodes.
> I implemented in genrestr the option to generate distance restraints between sets of atoms, e.g. between all C-alpha in a protein (which I'd like to use in the context of SAXS refinement), so there may be more applications.
> One way around the periodicity problem would be if the distance restraint code stored the distance vector from the previous step and then at the next application of the code checks whether the vector has flipped. This assumes the input structure should be correct..
. .. and there is already code that does exactly that, see groupcoord.cpp and its applications in e.g. the essential dynamics
and ion swapping modules.
> David van der Spoel, Ph.D., Professor of Biology
> Head of Department, Cell & Molecular Biology, Uppsala University.
> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
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