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I don't understand what you want exactly.<br>Your g_energy command does exponential averaging, that happens<br>on the printed data points. So there g_analyze or any program will do fine.<br>For the original data g_energy gives the exact standard deviation<br>over all MD steps, called RMSD.<br><br>But do you really want the standard deviation, or do you want<br>a standard error estimate?<br><br>Berk<br><br><hr id="stopSpelling">Date: Fri, 28 Aug 2009 09:30:37 -0300<br>From: fabracht1@gmail.com<br>To: gmx-users@gromacs.org<br>Subject: [gmx-users] Re: g_energy and g_analyze give different averages<br><br><div class="EC_gmail_quote"><div>Is there a correct way to obtain the standard deviation for these data sets?<br> </div><blockquote class="EC_gmail_quote" style="padding-left: 1ex;">
><br>
> Ragnarok sdf wrote:<br>
> > When analysing FEP simulations. After running g_energy -f fep000.edr -f2<br>
> > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I<br>
> tried<br>
> > to obtain the standard deviation for this ensemble average using<br>
> g_analyze<br>
> > -f runavg.xvg, but I've noticed that the average values are quite<br>
> different<br>
> ><br>
> ><br>
> g_energy takes all values during your simulation into account, g_analyze<br>
> only the printed datapoints.<br>
><br>
><br>
<br>
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