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Hi,<br><br>No, that assumes that all points are independent.<br>Which they might be, but they are usually not.<br><br>It is still not clear to me if you want the error of the exponential<br>difference of the error of the direct energies.<br><br>g_analyze -ee will give you an error estimate, but only based<br>on the printed points.<br><br>The simplest way is always to divide your set in 4 consecutive parts,<br>determine the averages with g_energy -b -e<br>and determine the error estimate through the method in Justin's link.<br><br>Berk <br><br>> Date: Fri, 28 Aug 2009 20:53:16 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] RE: Re: g_energy and g_analyze give different averages<br>> <br>> <br>> <br>> Ragnarok sdf wrote:<br>> > <br>> > <br>> > I am terribly sorry. I have not expressed myself well. I meant the <br>> > standard error of the mean energy given by g_energy. So I believe I <br>> > would like to know the standard error estimate.<br>> <br>> Based on the output RMSD (standard deviation), it seems rather straightforward <br>> to calculate SE:<br>> <br>> http://en.wikipedia.org/wiki/Standard_error_(statistics)#Standard_error_of_the_mean<br>> <br>> -Justin<br>> <br>> > <br>> > <br>> > I don't understand what you want exactly.<br>> > Your g_energy command does exponential averaging, that happens<br>> > on the printed data points. So there g_analyze or any program will<br>> > do fine.<br>> > For the original data g_energy gives the exact standard deviation<br>> > over all MD steps, called RMSD.<br>> > <br>> > But do you really want the standard deviation, or do you want<br>> > a standard error estimate?<br>> > <br>> > Berk<br>> > <br>> > Date: Fri, 28 Aug 2009 09:30:37 -0300<br>> > From: fabracht1@gmail.com <mailto:fabracht1@gmail.com><br>> > To: gmx-users@gromacs.org <mailto:gmx-users@gromacs.org><br>> > Subject: [gmx-users] Re: g_energy and g_analyze give different averages<br>> > <br>> > <br>> > Is there a correct way to obtain the standard deviation for these<br>> > data sets?<br>> > <br>> > <br>> > <br>> > <br>> > ><br>> > <br>> > > Ragnarok sdf wrote:<br>> > <br>> > > > When analysing FEP simulations. After running g_energy -f<br>> > fep000.edr -f2<br>> > <br>> > > > fep_000-005.edr for obtaining the dF = -kT ln <<br>> > exp(-(EB-EA)/kT) >A I<br>> > <br>> > > tried<br>> > <br>> > > > to obtain the standard deviation for this ensemble average using<br>> > <br>> > > g_analyze<br>> > <br>> > > > -f runavg.xvg, but I've noticed that the average values are quite<br>> > <br>> > > different<br>> > <br>> > > ><br>> > <br>> > > ><br>> > <br>> > > g_energy takes all values during your simulation into account,<br>> > g_analyze<br>> > <br>> > > only the printed datapoints.<br>> > <br>> > ><br>> > <br>> > ><br>> > <br>> > <br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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