I coded that up way back when by slightly displacing each atom along the x,
y, and z axis and creating a finite difference derivative from it. MD using
it heated up. The code for that is sitting in "folderol" on sourceforge if
you're inclined to look at it...
Scott
On Tue, Oct 4, 2011 at 12:38 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Oct 4, 2011 at 3:33 PM, Scott Le Grand <varelse2005.gmail.com
> >wrote:
>
> > As someone who wrote a *really* fast SASA approximation 18 years ago
> > (basically Shrake and Rupley on steroids), here's my two cents.
> >
> > The Still et al. approximation at the heart of GBSA has a correlation
> > coefficient of ~0.3 with the actual SASA. On the bright side, this
> > approximation has a derivative.
> >
>
> How bad would it be to use a non-analytical SASA approximation and just do
> numerical gradients?
>
> It would require doing a bunch of SASA calcs, but if it's fast enough it
> seems like it'd be fine (although it would slow the MD down a bit).
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Oct 04 2011 - 13:00:05 PDT
