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: [email protected] <mailto:[email protected]>
To: [email protected] <mailto:[email protected]>
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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--
========================================
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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