Hello David,
Thank you for the reference.
David M
On Mar 20, 2012, at 4:22 PM, David A Case wrote:
> 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
> 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
>
> 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.
>
> .....dac
>
>
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Received on Wed Mar 21 2012 - 07:30:02 PDT
