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 - 18:32:16 CDT

Actually I did a comparison for two simulations with explicit water
and explicit acetonitrile, respectively. The results are vastly
different. Based on your saying, GB is not the ideal model for my case
anyway since it might diminish the difference between water and
acetonitrile due to similarly high polarity.

-Eric

On 10/12/06, David A. Case <case_at_scripps.edu> wrote:
> On Thu, Oct 12, 2006, Eric Hu wrote:
>
> > If I understand correctly, there is no simply way to set up
> > acetonitrile GB parameters in current amber 9.
>
> Sure, it's simple to *do*: just set extdiel = 37. (or whatever) and run your
> jobs.
>
> What's not known is much about how accurate the results are expected to be.
> Since you would be doing something relatively new, you might have to be more
> alert than usual to strange behavior. But with such a high dielectric, I
> would expect reasonably decent results, i.e. not all that different from
> the types of errors/uncertainties that one sees with GB simulations in water.
>
> ...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