Adrian,
If I understand correctly, there is no simply way to set up
acetonitrile GB parameters in current amber 9. That's all I need to
know. Thanks.
-Eric
On 10/11/06, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
> Eric (and all),
> My understanding is that gb as parametrized in amber only for water.
> There are no parameters out there for other solvents, but I would like
> to know if I am wrong.
>
> Now: after that is said, there is a flag in gb called extdiel. It should
> be set to whatever your own solvent is. But, this still does not solve
> the parameters problem. I do not know if anyone has studied this
> carefully enough.
>
> Alexey Onufriev has 'new' versions of gb using a slightly different
> formalism, using parameters that should not depend on parameters for a
> particular solvent. He has published these methods in the last couple of
> years.
>
> Cheers
> Adrian
>
>
> Eric Hu wrote:
> > Dr. Case
> > Based on your experience, can you recommend a set of parameters to use
> > in that case? Thank you.
> >
> > -Eric
> >
> > On 10/11/06, David A. Case <case.scripps.edu> wrote:
> >> On Tue, Oct 10, 2006, Eric Hu wrote:
> >> >
> >> > I want to speed up my simulation with explicit organic solvent
> >> > (acetonitrile) model. Therefore I wonder if using implicit model might
> >> > accelerate the simulation significantly. And is there anyway to
> >> > introduce a GB model for any solvent in amber 9?
> >>
> >> GB has not been explicitly parameterized for acetonitrile, but might work
> >> work reasonably well (since this solvent has a fairly high dielectric
> >> constant). Whether or not you will see any speedups depends on the
> >> size of
> >> the system and other input parameters -- why not just try and find out
> >> for
> >> yourself?
> >>
> >> ...dac
> >>
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>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project and Department of Chemistry
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
> ============================================================================
>
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Received on Thu Oct 12 2006 - 20:36:15 PDT
