[gmx-users] Implicit solvent simulation

Erik Lindahl lindahl at cbr.su.se
Wed Jul 18 18:45:52 CEST 2007


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.

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!



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