# [gmx-users] RE: Re: g_energy and g_analyze give different averages

Justin A. Lemkul jalemkul at vt.edu
Sat Aug 29 02:53:16 CEST 2009

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Ragnarok sdf wrote:
>
>
> I am terribly sorry. I have not expressed myself well. I meant the
> standard error of the mean energy given by g_energy. So I believe I
> would like to know the standard error estimate.

Based on the output RMSD (standard deviation), it seems rather straightforward
to calculate SE:

http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean

-Justin

>
>
>     I don't understand what you want exactly.
>     Your g_energy command does exponential averaging, that happens
>     on the printed data points. So there g_analyze or any program will
>     do fine.
>     For the original data g_energy gives the exact standard deviation
>     over all MD steps, called RMSD.
>
>     But do you really want the standard deviation, or do you want
>     a standard error estimate?
>
>     Berk
>
>     Date: Fri, 28 Aug 2009 09:30:37 -0300
>     From: fabracht1 at gmail.com <mailto:fabracht1 at gmail.com>
>     To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     Subject: [gmx-users] Re: g_energy and g_analyze give different averages
>
>
>     Is there a correct way to obtain the standard deviation for these
>     data sets?
>
>
>
>
>      >
>
>      > Ragnarok sdf wrote:
>
>      > > When analysing FEP simulations. After running g_energy -f
>     fep000.edr -f2
>
>      > > fep_000-005.edr for obtaining the dF = -kT ln <
>     exp(-(EB-EA)/kT) >A I
>
>      > tried
>
>      > > to obtain the standard deviation for this ensemble average using
>
>      > g_analyze
>
>      > > -f runavg.xvg, but I've noticed that the average values are quite
>
>      > different
>
>      > >
>
>      > >
>
>      > g_energy takes all values during your simulation into account,
>     g_analyze
>
>      > only the printed datapoints.
>
>      >
>
>      >
>
>
>
>
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>
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--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

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