[gmx-users] Implicit solvent simulation

David van der Spoel spoel at xray.bmc.uu.se
Wed Jul 18 22:06:51 CEST 2007

steletch at jouy.inra.fr wrote:
> Selon Erik Lindahl <lindahl at cbr.su.se>:
>> 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 
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):

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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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