Hi Justin, When one issues g_energy –f *.edr –nmol X –b XXX, g_energy reads the frames from -f edr. file which is already written each nstenergy = 1000 steps for instance. So g_energy is not reading all MD steps. and I guess the same steps are printed to .xvg as out of g_energy. Please help me realize why g_energy is more accurate. I am confused :( Where are these all MD steps written that is stated in g_energy - h
Also : "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" By energy file we mean .edr file, right? Why does it say *energy file* contain averages over all MD ...than the number of frames in *energy file*?! I am not able to differentiate between energy file and energy file? Please help! Sorry for naive questions! On 21 February 2013 19:23, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 2/21/13 6:58 PM, Juliette N. wrote: > >> 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! >> > > See the message below, printed by g_energy. > > >> 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. >> * >> > > The following section explains the discrepancy in your results: > > 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<http://manual.gromacs.org/online/xvg.html> >> >output >> >> > Thus, the only way to achieve absolute agreement between .xvg and .edr > analysis is to set nstenergy = 1, which will result in really big .edr > files, and the difference in practice should be pretty small. > > > 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... >> >> > Well, there are default values that are used for -nbmin and -nbmax, so if > you don't specify any values manually, those are used. The default is 5. > Without looking into the code, it would seem that block averaging of some > sort is being done. The error estimate for g_analyze -ee is documented > more thoroughly and is described in the paper mentioned in the help > description. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
