[EMAIL PROTECTED] wrote:
Selon Erik Lindahl <[EMAIL PROTECTED]>:
Hi,
On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
The version used by Alan Mark has never made it into gromacs.
Rather, Erik Lindahl started the implementation of this stuff but
did never finish it completely, due to other priorities I presume.
We should however take out the variables to avoid confusion (unless
someone provides a full implementation).
Actually, technically the GB implementation is already in Gromacs
(even assembly kernels), and quite correct, it's just that you don't
have the born radii yet :-)
The last couple of years we've mainly done membrane stuff where it's
not useful for my students, and thus not a priority to implement.
However, recently Per Larsson has finished C implementations of the
Still radius calculations that I've started optimizing.
The big remaining task is the SA part of GB/SA, i.e. the surface
calculation, which also needs to be optimized and preferrably
parallelized (harder) to be useful.
Erik, didn't you say once that you implemented fast area calculations
and derivatives?
It's an interesting CS problem, but there certainly are at least a
couple of papers on these topics.
Fan Hao actually offered us the code he wrote with Alan, but the
challengefor us isn't to write a trivial Still GB implementation, but
to make it perform well. There's little point in having a GB
implementation that is slower than the fast explicit-solvent
simulations in Gromacs!
Happy to hear that, if you need some beta-tester for validation and performance
tests, i'm your man :-)
You can help already now, by heading over to
http://wiki.gromacs.org/index.php/Implicit_Solvent
and adding more documentation.
Although I realize it is the holiday season, at least in Europe, I would
like to once more recommend the development wiki for documenting this
kind of discussion, and for publishing specifications for algorithms,
like (totally unrelated, but came up earlier today):
http://wiki.gromacs.org/index.php/Cpp_replacement
Cheers,
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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