[gmx-developers] Monte Carlo Simulations

David van der Spoel spoel at xray.bmc.uu.se
Wed Feb 1 13:23:39 CET 2012

On 2012-02-01 09:38, Anton Feenstra wrote:
> Hi,
> Just plugging in our work, since I believe it will be relevant ;-)
> (and my apologies if it turns out not so)
> A post-doc in our group, René Pool, has implemented a grand-canonical
> Monte Carlo scheme using the GromPy gromacs-python interface. It is
> based on library calls to the gromacs md engine from python, and
> therefore can be very flexible. In our tests, it is just about as
> efficient as a fully gromacs-internal implementation could be (i.e., the
> overhead due to python etc, it only a few percent).
> There is an open source repo for GromPy
> at gitub: https://github.com/GromPy
> There's a paper coming out in JCC soon, describing the interface and its
> performance in calculating the critical properties of a LJ system and of
> SPC water:
> Enabling Grand-Canonical Monte Carlo: Extending the Flexibility of
> GROMACS Through the GromPy Python Interface Module
> René Pool, Jaap Heringa, Martin Hoefling, Roland Schulz, Jeremy C.
> Smith, and K. Anton Feenstra

Dear Anton, this looks really useful. It would be even more useful if it 
could be employed with bleeding edge versions of gmx. In particular, I 
would be interested in running tons of small simulations and edit the 
tpr files in memory meanwhile. Do you think this kind of integration 
will be possible in the near future? I'm asking in particular since the 
gromacs you are using is somewhat dated (but for my purpose I would need 
the 4.6 development branch).

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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