Re: [AMBER] How to calculate PMF using Jarzynskiís equality?

From: Adrian Roitberg <roitberg.ufl.edu>
Date: Tue, 29 Jan 2013 11:39:03 -0500

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 Jarzynskiís equality to get the final estimate of the free
>> energy difference?
>>
>> Hope this helps,
>> Cuiyl
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>

-- 
                            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
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