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

[Berk Hess]

Hi,

No, that assumes that all points are independent.
Which they might be, but they are usually not.

It is still not clear to me if you want the error of the exponential
difference of the error of the direct energies.

g_analyze -ee will give you an error estimate, but only based
on the printed points.

The simplest way is always to divide your set in 4 consecutive parts,
determine the averages with g_energy -b -e
and determine the error estimate through the method in Justin's link.

Berk 

> Date: Fri, 28 Aug 2009 20:53:16 -0400
> From: jalemkul at vt.edu
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] RE: Re: g_energy and g_analyze give different averages
> 
> 
> 
> Ragnarok sdf wrote:
> > 
> > 
> > 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.
> 
> Based on the output RMSD (standard deviation), it seems rather straightforward 
> to calculate SE:
> 
> http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean
> 
> -Justin
> 
> > 
> > 
> >     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 <mailto:fabracht1 at gmail.com>
> >     To: gmx-users at gromacs.org <mailto: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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> -- 
> ========================================
> 
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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