[gmx-users] MBAR bootstrap

[Michael Shirts]

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.le at 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
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