True, I found the lower bin numbers makes the error change (increase), especially at ends of the run, howevere the mean values were the same. I also checked with g_sham as comparision, and found again the means the same but differences in error (max and min values if I include all data). So all three checks gave same mean, different (wider or lower) error (and I guess subsequent varience so is expected).
Interesting note, if I use sham, or wham, running wham on only a single trajectory, then merge them all by hand in a spread sheet (wham output), the wham has the same values as the sham? Does anyone know why? Stephan Watkins -------- Original-Nachricht -------- > Datum: Thu, 26 Jul 2012 06:46:04 -0400 > Von: Justin Lemkul <jalem...@vt.edu> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] Bins in wham analysis > > > On 7/26/12 3:55 AM, neeru sharma wrote: > > Dear Gromacs users, > > > > I have a query regarding the number of bins used in wham analysis. > > > > If I have performed by simulations over 15 umbrellas (15 different > > staring structures), what should be the ideal number of bins to > > perform wham analysis? Does it depend on the number of umbrellas. For > > example: > > > > 1) Should I use more than 15 bins in my case, and the one that gives > > proper overlap in histogram ? > > 2) Or any number of bins (even if it is less than 12) can be used, if > > I get proper overlap in my histogram output? > > > > Any suggestion is appreciated. > > > > The -bins option has to do with the final PMF profile. The default value > is > 200, and I would think that setting a low number like 12 or 15 would > result in > very poor output. I believe there is some discussion on this in the > g_wham paper. > > -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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 * Only plain text messages are allowed! * 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
