This is not the right place to ask about MBAR. You could pose the question on https://github.com/choderalab/pymbar if you have specific questions about how to implement something there. https://github.com/MobleyLab/alchemical-analysis is a wrapper for MBAR that can process gromacs files.
See: http://www.alchemistry.org/wiki/Analyzing_Simulation_Results#Bootstrap_Sampling for a discussion of bootstrap sampling in the context of free energies. On Tue, Jan 9, 2018 at 8:01 PM, Thanh Le <thanh.q...@sjsu.edu> wrote: > Hi everyone, > I have a question regarding using bootstrap for MBAR. > After running 30 windows for the complex and 20 windows for the ligand, > 100 ns each, I have a problem trying to do bootstrap (based on what I have > read, bootstrap sampling is recommended to analyze results from MBAR) > Can anyone point me to the correct direction to implement bootstrap? Or > any advice on how to analyze MBAR? > Thanks, > Thanh Le > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.