Hi Kirtana,
I'm not sure what you mean by fixed as I haven't done Umbrella sampling
with AMBER before, but you certainly don't want to artificially fix it in
place, as they will affect its degrees of freedom in a manner that is
independent of the umbrella sampling.
What you should be trying to do, is to apply a harmonic restraint (a
spring) between say the two alpha-carbons in your residues of interest.
You will end up having many simulations, each representing a "window" in
which you step along the distance (going from small to large) while also
having to potentially change the force constant for the harmonic restraint
depending on how the system behaves.
You might also want to consider using ABMD (which is outlined in the
AMBER11 manual) to get a rough but quick idea of what your PMF might look
like.
~Aron
On Wed, Feb 15, 2012 at 5:34 PM, kirtana S <skirtana4.gmail.com> wrote:
> Dear Amber Users,
>
> I want to do umbrella sampling to obtain the potential of mean force with
> distance between the residues as the reaction cordinate. The example
> discussed uses dihedral restraints. Should I use distance restraints by
> keeping one residue fixed.Please suggest .
>
> Thanks
> Kirtana
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--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Feb 15 2012 - 15:00:02 PST
