Well, you could try different implicit solvation models. The manual goes
into some detail about these, igb=5,7 and such. I'm not an expert, but I'm
not sure that you are necessarily going to see better agreement, it's a
huge change to go from explicit to implicit solvation.
On Sat, Mar 17, 2012 at 12:29 AM, Aditya Padhi <adi.uoh.gmail.com> wrote:
> Dear Amber users,
> I want to run Implicit solvent MDs with my protein of interest. I
> have already simulated the protein using explicit water model TIP3P. I want
> to yield the results in better agreement/ similar conformations like that
> of explicit solvent runs. But I am not getting the same results. Can any
> one please suggest what are the best parameters to achieve results using
> implicit solvent that can mimic the results of explicit solvent MD runs?
>
> Thanking you,
> Regards
> Aditya.
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Fri Mar 16 2012 - 23:00:03 PDT
