AMBER Archive (2008)

Subject: Re: AMBER: igb and ibelly

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Fri May 30 2008 - 17:36:03 CDT

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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