AMBER Archive (2006)

Subject: Re: AMBER: generalized born model for organic solvent

From: Eric Hu (list.eric_at_gmail.com)
Date: Thu Oct 12 2006 - 12:47:44 CDT

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_at_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_at_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
> >>
> >> -----------------------------------------------------------------------
> >> The AMBER Mail Reflector
> >> To post, send mail to amber_at_scripps.edu
> >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >>
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber_at_scripps.edu
> > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> >
>
>
> --
> 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_at_qtp.ufl.edu
> ============================================================================
>
> To announce that there must be no criticism of the president,
> or that we are to stand by the president right or wrong,
> is not only unpatriotic and servile, but is morally treasonable
> to the American public."
> -- Theodore Roosevelt
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu