You could also reconstruct such a surface from some other enhanced sampling
method such as accelerated MD or temperature replica exchange (or both
together!). The ensuing analysis is likely not available in a standard
program and is technically advanced, but there are tools available such as
the pymbar implementation of MBAR:
https://github.com/choderalab/pymbar
Regards,
Brian
On Mon, May 5, 2014 at 7:25 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Tue May 06 2014 - 07:00:02 PDT
