[gmx-users] error estimates of free energy calculations

Berk Hess gmx3 at hotmail.com
Wed May 16 07:47:18 CEST 2007

>From: "David Mobley" <dmobley at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] error estimates of free energy calculations
>Date: Tue, 15 May 2007 15:55:01 -0700
>>However, in my opinion (assuming the total error should be calculated
>>from standard error propagation), the way g_analyze calculates the
>>total error is incorrect. It results in an overestimation of this
>>total error by at least a factor of sqrt((number of lambda points) -
>>1). This factor is 4.5 in my case, accounting for the larger part of
>>my previoulsy mentioned loss of accuracy. And indeed, as you guys
>>already mentioned, the remaining part may be explained from the fact
>>that Berk uses twice as many lambda values.
>Whoops! Justifies my paranoia about using other people's analysis
>tools. :) The person responsible for the analysis tool should take a
>look at this -- if the tool does error analysis for the integral, it
>should do it properly.

ah, g_analyze indeed seems to print an error estimate of the integral,
I didn't know about this.
But according to me this is totally wrong.
It divides the sum of variances by n-1, whereas this should be n^2.

I'll fix it for the next release.


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