I can imagine creating a pmf from a histogram of population vs Q for
converged ensembles. What's much harder to imagine is implementing Q as a
coordinate for something like umbrella sampling. On top of being
discontinuous, it would be counterproductive since it would strongly hinder
the sampling orthogonal to Q.
On May 5, 2014 6:50 PM, "Nihal Korkmaz" <enihalkorkmaz.gmail.com> wrote:
> Dear Amber Community,
>
> I am aiming to implement Q (fraction or number of native contacts) as a
> reaction coordinate for PMF just like we conventionally use distance or
> angle restraints.
>
> If there is anyone tackled/attempted this issue before, I appreciate any
> suggestions.
>
> Best,
> Nihal
>
> --
> E. Nihal Korkmaz
> UW-Madison, Biophysics Program
> Qiang Cui Lab
> Phone: 608-265-3644
> E-mail: korkmaz.wisc.edu
>
>
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Received on Mon May 05 2014 - 16:30:03 PDT
