[gmx-users] waterbug fixed + infinite systems support improved
spoel at xray.bmc.uu.se
Sun Sep 7 17:10:02 CEST 2003
Dear GROMACS users and developers.
This is to let you know that it seems like the water bug (involving
parallel simulations with no water on the first processor) now has been
resolved in the CVS version of gromacs.
In addition I have improved the support for infinite systems, like
nanotubes, or crystalline systems. Previously one had to set an
environment variable (GMXFULLPBC) and would still get lots of error
messages (and probably incorrect resultsfor at least the 1-4
interactions). Now there is an mdp option
pbc = full
that implements this feature correctly. Note that the full option should
give the same results as xyz, but in theory be a bit slower (few %). I
would also like reports on the relative performance of the options.
In order to use these improvements you will at current have to download
the CVS tree (see http://www.gromacs.org/developer/cvs_usage.php for
Obviously feedback is very welcome, as we are approaching another point
release, and these were the most important remaining bugs as I see it.
Please go ahead and test it!
Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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://xray.bmc.uu.se/~spoel
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