Hi Cuiyl,
I've never done such a calculation myself, but my understanding is that
they can be quite similar to WHAM/MBAR calculations. The latest development
that I am familiar with is this paper:
Minh, D. and Chodera, J. Optimal estimators and asymptotic variances for
non-equilibrium path-ensemble averages J. Chem. Phys. 2009, 131, 134110.
Regards,
Brian
On Tue, Jan 29, 2013 at 3:34 AM, Cuiyl <cuiyinglukitty.gmail.com> wrote:
> Dear Amber Users:
>
> I've done some SMD simulations with different starting coordinates
> taken from equilibrium simulations. The output dist_vs_t files contain the
> work of pulling from the initial distance to the final distance. I didn't
> use umbrella sampling and WHAM. Once the work is computed, how can I
> average it using Jarzynski’s equality to get the final estimate of the free
> energy difference?
>
> Hope this helps,
> Cuiyl
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--
================================ 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
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Received on Tue Jan 29 2013 - 09:00:03 PST
