[gmx-users] error estimates of free energy calculations
Berk Hess
gmx3 at hotmail.com
Wed May 16 07:50:59 CEST 2007
>From: "Berk Hess" <gmx3 at hotmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: Re: [gmx-users] error estimates of free energy calculations
>Date: Wed, 16 May 2007 07:47:18 +0200
>
>
>
>
>>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.
>
>Berk.
Also it does not take into account unevenly spaced x values.
Sorry that I accuses Jeroen of incorrect integration...
Berk.
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