The simplest way is, for a given value of your pulling coordinate, to do:
<exp^(work/kT)> where the average is over the different runs you have done
that average should give you exp(-deltaG(x)/kT)
adrian
On 1/29/13 11:36 AM, Brian Radak wrote:
> 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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>>
>
>
--
Dr. Adrian E. Roitberg
Professor
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
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Received on Tue Jan 29 2013 - 09:00:04 PST
