Hi Matthew, Thanks for your reply. I tried g_analyze as you suggested:
1) I am wondering why the average given by g_energy and g_analyze are not identical. I tried the following: g_energy -f Potential. edr -o Potential.xvg and extracted the average then provided Potential.xvg as input to g_analyze ( I did this since g_analyze seems to read xvg files only). and issued: g_analyze –f.Potential.xvg–av. However the averages are not identical. 2) Also I tried g_energy -f Potential. edr -o Potential.xvg and from g_energy I can see Energy Average *Err.Est.* RMSD Tot-Drift are given by default. Then tried g_analyze -ee and noticed that the * Err.Est.* reported by g_energy and the one from g_analyze -ee are not identical! Could you please explain why is this happening and how *Err.Est.* is estimated? . g_energy says: An error estimate of the average is given based on a block averages over 5 blocks using the full-precision averages. The error estimate can be performed over multiple block lengths with the options -nbmin and -nbmax. * Note* that in most cases the energy files contains averages over all MD steps, or over many more points than the number of frames in energy file. This makes the g_energy statistics output more accurate than the .xvg<http://manual.gromacs.org/online/xvg.html>output I cant seem to understand how error is obtained.:( If I am reading the frames from say , -b 4000 -5000, what happens if I dont provide blocks etc... Appreciate your comments, Thank you, Cheers J. * * On 21 February 2013 10:48, Matthew Zwier <mczw...@gmail.com> wrote: > Hi, > > I don't know of a GROMACS tool to do this. g_analyze may work (see manual > page, option "-ee"), if you can generate a time series of A to look at. > > That said, what you've described is a classic propagation of error problem. > If uncertainties are small and likely to be symmetric about the mean, then > you can analytically calculate the uncertainty in A in terms of the > uncertainties on the input quantities. If the uncertainties are not small > or are very asymmetric about the mean, then something like bootstrapping > may be in order. Information on both of these is readily available on the > web (now that you have a few keywords to search for). > > Cheers, > Matt Zwier > > > On Thu, Feb 21, 2013 at 2:09 AM, Juliette N. <joojoojo...@gmail.com> > wrote: > > > Hi everyone, > > > > Does anyone know of a gmx tool which calculates the statistical > > uncertainty? > > > > and if there is such a tool, how can one calculate the statistical > > uncertainty for a quantity A (not extractable directly by gromcas), which > > is expressed in terms of 3 other quantities, e.g. property A=(Potential > of > > gas phase - potential of liquid phase)*(density of liquid phase). > > > > I am interested in statistical uncertainty of A. > > > > Appreciate your help, > > -- > > Thanks, > > Best, > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Thanks, J. N. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
