[gmx-developers] Re: file headers & nblists

Vishal Vaidyanathan vvishal at stanford.edu
Wed Jun 12 21:28:11 CEST 2002

  The SASA model I am using is a very cheap and common one created by
Still and co-workers. It needs two loops over all pairs - one to calculate
the areas and one to calculate the derivatives - because of the form of
the energy function, it is not possible to do both in one loop over all
pairs. So a neighbour list would improve things even if we are simulating
without explicit solvent. The GBSA method you mention has been implemented
with the same SASA in the TINKER package. But I will also be putting in a
few other SASA methods as well as GB, PB (poisson-boltzmann solvers) and a
few other options into gromacs while I'm at it so that it would be
possible to explore very fast and approximate implicit methods as well as
more accurate models that may even be slower than explicit solvent for a
single energy calculation.
  Have fun!

> Which SASA model will you use?
> I have the same problem as you since the Richmond's model is precise
> but quite slow. The cut-off method can be a good solution to that.
> But there are other analytical models which are fast. You can get
> approximated SASA without having cut-off.
> Best regards
> sincerely
> Hao Fan :-)
> -------------------------------------------------------------------------
> Drs. Hao Fan                            email F.Hao at chem.rug.nl
> Lab. of Biophysical Chemistry
> University of Groningen
> Nijenborgh 4                            9747 AG GRONINGEN
> The Netherlands
> -------------------------------------------------------------------------

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