<br><br><div class="gmail_quote">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.<br><div class="gmail_quote">
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<br>
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>
Date: Fri, 28 Aug 2009 09:30:37 -0300<br>
From: <a href="mailto:fabracht1@gmail.com" target="_blank">fabracht1@gmail.com</a><br>
To: <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
Subject: [gmx-users] Re: g_energy and g_analyze give different averages<div><div></div><div class="h5"><br>
<br>
Is there a correct way to obtain the standard deviation for these data sets?<br>
<br>
<br>
<br>
<br>
><br>
<br>
> Ragnarok sdf wrote:<br>
<br>
> > When analysing FEP simulations. After running g_energy -f fep000.edr -f2<br>
<br>
> > fep_000-005.edr for obtaining the dF = -kT ln < exp(-(EB-EA)/kT) >A I<br>
<br>
> tried<br>
<br>
> > to obtain the standard deviation for this ensemble average using<br>
<br>
> g_analyze<br>
<br>
> > -f runavg.xvg, but I've noticed that the average values are quite<br>
<br>
> different<br>
<br>
> ><br>
<br>
> ><br>
<br>
> g_energy takes all values during your simulation into account, g_analyze<br>
<br>
> only the printed datapoints.<br>
<br>
><br>
<br>
><br>
<br></div></div></blockquote></div><br>
</div><br>