Macs in Chemistry

Insanely Great Science


Flare™ V4 release


About a year ago I wrote a review of Flare a tool for structure-based drug design.


The key new features of Flare V4 includes significant improvements to Free Energy Perturbation (FEP), new and improved force fields, new Dynamics analysis tools, plus new and improved GUI functionality.

The implementation of the Open Forcefield now allows users to update themselves.

FEP has been implemented in Flare DOI and this release improves performance.

In terms of speed, all FEP calculation in Flare V4 are significantly faster thanks to an improved algorithm with a 20% increase in performance, and they are fully parallelizable. This means that each bit of the transformation of one compound into another (the lambda windows) can be run on separate GPUs: the results will be merged at the end of the calculation. This can bring the calculation time for a single transformation on a medium-sized protein to less than 2 hours on a small cluster of 10 GPUs (for example AWS g4dn.xlarge, Tesla T4 spot instances).




The Open Force Field Initiative is an open source, open science, and open data approach to better force fields. All the code is on GitHib and they also provide highly curated datasets.

The idea is to enable molecular mechanics on small and macromolecules jointly using open and freely available software.

A recent blog post from Peter Schmidtke caught my eye.

Recently a few updates of the openforcefield toolkit came out … a game changer, as you’ll see.

The work investigated whether the 768 fragments from the XChem fragment library at Diamond can be parametrised with the new version of Open Force Field (0.4) and how they behave after a simple minimisation.

In short all fragments technically pass the parametrisation and minimisation step, this was supported by visual inspection.

All the code is on GitHub.