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

André Farias de Moura moura at ufscar.br
Tue Mar 17 19:40:48 CET 2020


Dear Alex,

in a nutshell: yes, convergence might not have been achieved even if the
estimated error bars seem small.

maybe this reference might be helpful:

https://doi.org/10.1016/j.bbamem.2016.03.006

best,

Andre

On Tue, Mar 17, 2020 at 2:14 PM Alex <alexanderwien2k at gmail.com> wrote:

> 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
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090


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