Hi Prof. Case,
This is perfect for me to read because I'm interesting in possibly reducing run time by cutting down
on the force evaluations using frozen atoms.
Thank you,
Holly
> On Fri, May 30, 2008, Holly Freedman wrote:
>
> > Can someone please explain to me why it is that the ibelly option is not
> > allowed with igb>0 (Generalized Born)? I don't understand how the two
> > options are connected.
>
> Since GB is not a pairwise theory, it is not a simple matter to simply try to
> ignore certain atoms. A discussion of what would be involved, and the
> approximations required, is given here:
>
> %A O. Guvench
> %A J. Weiser
> %A P. Shenkin
> %A I. Kolossvary
> %A W.C. Still
> %T Application of the Frozen Atom Approximation to the GB/SA Continuum Model
> for Solvation Free Energy
> %J J. Comput. Chem.
> %V 23
> %P 214-221
> %D 2002
>
> These ideas have never been implemented in Amber.
>
> You can set ntr=1 and restrain atoms to be (very) near to their starting
> points.
>
> [Aside: I've long been in favor of removing ibelly for any purpose in Amber,
> but it hasn't been a high priority, and people seem to have some use for that
> facility, so it still sticks around.]
>
> ...dac
>
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--
Department of Physics, University of Alberta
Edmonton CANADA
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Received on Sun Jun 01 2008 - 06:08:06 PDT
