[gmx-users] RE: Re: g_energy and g_analyze give different averages
Ragnarok sdf
fabracht1 at gmail.com
Sat Aug 29 02:45:37 CEST 2009
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: 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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