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.
> > 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: fabrac...@gmail.com > To: gmx-users@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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