[gmx-users] Fwd: Reproducibility of a PMF plot

[Alex]

Any comment, please?

Thank you,
Alex

---------- Forwarded message ---------
From: Alex <alexanderwien2k at gmail.com>
Date: Sun, Mar 15, 2020 at 8:16 PM
Subject: Reproducibility of a PMF plot
To: <gmx-users at gromacs.org>


Dear all,

Of course it is always good to prove that a MD simulation is reproducible
by repeating several replicas of a simulation and then average over the
quantity of interest, specially for a publishable result.
I wonder if that also is necessary for a potential of mean force (PMF)
calculation using umbrella sampling in which the bootstrap analysis is
performed to calculate the standard deviation?
Or for an alchemical free energy calculation where the e.g. the block
averaging is used?

Regards,
Alex