Raphael Alhadeff wrote: > Hello everyone, > > I wanted to ask if anyone knows how to compute standard deviation, for the > sake of adding error bars to an energy profile output using g_wham (PMF using > umbrella sampling in my case). > > Just to clarify, I am talking about the deviation of the energy profile on > ONE simulation (composed of 25 "windows" in my case, with overlap but no > repeats).
Hi Raphael, there is a new g_wham available in the most recent gromacs version. It is able to do bootstrapping. (check g_wham -h) To get hopefully reliable error bars you need more umbrella histograms and make sure that they are really independent. The new g_wham supports bootstrapping of complete histograms (which are more likely to be indpendet than consecutive simulations frames of one umbrella window simulation.) If you do bootstrapping from frames *within* one umbrella histograms you will in some cases drastically underestimate the error because of hidden long autocorrelations. Note that if you simulate a protein you most often have long autocorrelations and it is difficult to estimate the autocorrelation times. Cheers, Jochen Btw, if you encouter problems with the new g_wham please report them to me. Thanks. > > Thanks in advance, > Raphael > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- ************************************************ Dr. Jochen Hub Max Planck Institute for Biophysical Chemistry Computational biomolecular dynamics group Am Fassberg 11 D-37077 Goettingen, Germany Email: jhub[at]gwdg.de Tel.: +49 (0)551 201-2312 ************************************************ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
