Hi Aron,
I have tried with igb=5, but not achieved any desirable conformations
of my protein of interest as compared to Explicit solvent MD runs. I will
try with igb=7 and different parameters. If you have any other suggestions,
then do let me know.
Thanking you,
Regards
Aditya.
On Sat, Mar 17, 2012 at 11:23 AM, Aron Broom <broomsday.gmail.com> wrote:
> 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 - 23:00:04 PDT
