Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method

From: Hannes Loeffler <>
Date: Wed, 17 May 2017 10:12:44 +0100

On Wed, 17 May 2017 09:00:54 +0000
Ramin Salimi <> wrote:

> Hi Hannes
> You, in fact, are right since the free energy difference is equal to
> the average work plus the second cumulant expansion, but we do not
> have the free energy difference so amongst the three quantities, we
> only have the average work, not either the variance or the free
> energy difference???

The equality only holds when the distribution of the work values is a
Gaussian which e.g. when you operate in a near-equilibrium regime, see
for instance .

The variance here is the variance of your work values! E.g. paste all
work values that you have received from N simulations into a spread
sheet and ask it to compute the sample variance (like the function
var.S in Excel/LibreOffice calc) from this data. That's really just
standard statistics.


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Received on Wed May 17 2017 - 02:30:03 PDT
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