[gmx-developers] Non Equilibrium alchemy implementation in gromacs

Piero Procacci piero.procacci at unifi.it
Sat Dec 15 18:25:04 CET 2018

> The main novelty of the paper in my opinion is the usage of
> statistical efficiency to compare different methods. It could well be
> that more efficient methods than MBAR can be devised but without
> efficiency measure, how are we to judge which method is more
> efficient?

You are definetely right. However, efficiency is meaningless without
reproducibility. For the molecular set you have used (rigid and small
molecules) reproducibility is not a problem whether one uses FEP or NE
techniques.  However do you feel that your conclusions on
computational efficiency for benzene or ethanol hydration energies
apply unscathed to monsters such as the MCL1 inhibitor S63845 (
https://www.apexbt.com/s63845.html )?

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