[gmx-users] g_energy averages
David L. Bostick
dbostick at physics.unc.edu
Wed Jul 17 20:44:09 CEST 2002
Okay thanks..
so I guess I want to ask from my pasted previous example.. though perhaps
it cannot be classified as an "error." In the sense that the average
surface tension <#Surf*SurfTen> is taken over 250000 steps even if
nstenergy is 500, then the standard deviation of the mean of this is
2263.84/sqrt(250000)
and not
2263.84/sqrt(500) .. i.e. 500 = 250000/500
for brevity.. I just want to be sure that g_energy takes ALL of the steps
for averaging or just the subset that you specify with nstenergy. From the
manual, I understand that ALL of them are used. I just want validation on
this.
Thanks
David
> > If I get from the energy file
> > Energy Average RMSD Fluct.
> > #Surf*SurfTen 147.805 2270.69 2263.84
> >
> > and the run was over 250000 steps, the standard error is
> >
> > 2263.84/sqrt(250000)
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David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
On 17 Jul 2002, David wrote:
> On Wed, 2002-07-17 at 20:15, David L. Bostick wrote:
> >
> > .. So, if I want to find the standard error in an average value, I just
> > take the fluctuation and divide it by sqrt(nsteps)?
> >
> > i.e.
> > If I get from the energy file
> > Energy Average RMSD Fluct.
> > #Surf*SurfTen 147.805 2270.69 2263.84
> >
> > and the run was over 250000 steps, the standard error is
> >
> > 2263.84/sqrt(250000)
> No you should divide by the sqrt of the number of *independent* data
> points. For energy, there is a correlation on the order of a few
> picoseconds (depends on system). For e.g. the dipole moment of the box
> it is usually 10 ps (can be related to Debye relaxation). g_analyze may
> help you estimating errors, but it is not trivial...
>
>
> --
> Groeten, David.
> ________________________________________________________________________
> Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576, 75123 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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