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

Berk Hess gmx3 at hotmail.com
Fri Aug 28 14:59:54 CEST 2009

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?


Date: Fri, 28 Aug 2009 09:30:37 -0300
From: fabracht1 at gmail.com
To: 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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