[gmx-users] error estimates of free energy calculations
David van der Spoel
spoel at xray.bmc.uu.se
Wed May 16 08:12:57 CEST 2007
Berk Hess wrote:
>
>
>
>> 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
>>
>> Jeroen,
>>
>>> 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.
>
It is the standard deviation, rigth? Which is what the source code says
it is...
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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