Re: [AMBER] Fast ibelly?

From: David A Case <>
Date: Tue, 20 Mar 2012 16:22:15 -0400

On Tue, Mar 20, 2012, David Minh wrote:
> Unfortunately, it seems like their [NAMD's] implementation
> of OBC generalized Born doesn't take advantage of fixed atoms, as
> it is only marginally faster than a fully flexible implicit solvent
> simulation.

This is a fundamental problem, and is basically the reason why we don't try to
support belly with igb>0: you don't save much time. The issues are discussed

%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

This paper discusses a possible workaround to allow frozen atom calculations
in GB. But it's not trivial, and has not been pursued (as far as I know)
by anyone in the Amber community.


AMBER mailing list
Received on Tue Mar 20 2012 - 13:30:03 PDT
Custom Search