[gmx-users] error estimates of free energy calculations

David van der Spoel spoel at xray.bmc.uu.se
Wed May 16 07:41:29 CEST 2007

David Mobley wrote:
> 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.
Will do. Of course this is why you get the source code so you can check 
it. Try that with excel. And actually the source code says that what you 
are getting is the standard deviation rather than the standard error. It 
should have been in the documentation of course.

Check your input
Check your output

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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