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

From: Ramin Salimi <>
Date: Wed, 17 May 2017 09:00:54 +0000

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???

From: Hannes Loeffler <>
Sent: Wednesday, May 17, 2017 3:52:54 AM
Subject: Re: [AMBER] Statistically estimating the error and data reliability for Jarzynski Method

To answer some of your questions: the first cumulant is simply the
"normal" average of the work values, while the second cumulant is the
variance from all your work values. This is standard statistics so
there is not really a need for a specific AMBER tool I would think.

On Wed, 17 May 2017 08:24:54 +0000
Ramin Salimi <> wrote:

> Hi Amber Users
> I have a few questions about calculating the variance and error of
> the Steered MD/Jarzynski Method:
> 1- Having completed the SMD, how to calculate the second cumulant
> expansion to see how different it is from the full Jarzynski average?
> 2- How should I check the variance between the replicates at the end
> of the pull? Does it mean that I should take the arithmetic average
> of the work values, corresponding to different iterations, at each
> extension and then calculate the variance corresponding to the set of
> work values for a particular extension? If yes, then we would have
> many variances corresponding to a particular extension, which does
> not make much sense to me.
> 3- Can we compute the variance, or standard deviation, and second
> order cumulant expansion in Amber? I mean does it have the capability
> of computing these as well?
> 4- How different is it from the Jarzynski method, that basically
> works on a reaction coordinate i.e. the distance between the atoms or
> groups of atoms, when we use ntr to freeze one atom or a group of
> atoms, and pull the other end with a different potential? I mean what
> difference does it make in results? which one is better to use? I
> would want to learn how different the physics of the problem would be
> for I am used to see only constant force constants in SMD.
> I would really appreciate any help.
> Regards
> Ramin
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Received on Wed May 17 2017 - 02:30:03 PDT
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