diff --git a/_posts/2025-10-23-release-v1.7.md b/_posts/2025-10-23-release-v1.7.md new file mode 100644 index 0000000..58c9eb3 --- /dev/null +++ b/_posts/2025-10-23-release-v1.7.md @@ -0,0 +1,61 @@ +--- +layout: post +title: "OpenFE v1.7: SepTop, ABFEs, faster simulations, and more!" +categories: science update +--- + +We are pleased to announce the release of **openfe** version 1.7.0! + +This release brings along some long-awaited features, notably including new Protocols (SepTop & ABFEs), and performance improvements. + +Please see below for some highlights and see the [Changelog][] for more details. + +## New alchemical simulation protocols + +### Separated Topologies + +We include a new relative binding free energy protocol based on the Separated Topologies (SepTop) method, as defined by [Rocklin et al.][] and [Baumann et al.][]. +Using SepTop, you can calculate the difference in binding free energy between two ligands by essentially performing two absolute binding free energy calculations simultaneously in opposite directions. + +Crucially, this avoids the needs for creating a hybrid topology, **making atom mapping unnecessary and allowing for scaffold hopping!** + +Please see our [SepTop tutorial][] for a demonstration on how to use it! You can also read more about the method in our [SepTop user guide][] entry. + +### Absolute Binding Free Energies + +We also include a new Absolute Binding Free Energy (ABFE) protocol, based on a partial annhilation scheme. This method allows for the direct calculation of binding affinities by alchemically removing a ligand from its binding site. + +Please see our [ABFE tutorial][] and associcated [ABFE user guide entry][] to see how to use the method. + +## Performance improvements through better default settings + +We have updated our default settings to maximize the performance of `openfe`, leading to a **~2x performance improvement compared to the v1.0 release!** + +The figure below shows the average performance of a single thermodynamic cycle for a pairwise transformation using our relative binding free energy hybrid topology protocol. We see see a drop from ~6 hours to ~3 hours by switching our default settings and moving to OpenMM 8.2. This can be further improved by layering multiple simulation using the [NVIDIA multi-processing service][] + +
average cost of a ligand pair alchemical cycle over the JACS set.
+ +These settings updates mostly involve moving away from overly conservative parameters to ones that are more widely used in production settings. These include: + * Switching from a cubic box to a dodecahedron box for solvation, avoiding excess waters. + * Increasing the replica exchange rate to 2.5 ps (from 1 ps), reducing performance losses linked to GPU context switches. + * Reducing the nonbonded cutoff from 1.0 nm to the OpenFF recommended value of 0.9 nm. + +These new default settings were extensively validated on RBFE and AHFE simulations, showing little to no difference against the previous defaults. + +## Installing `openfe v1.7.0` + +`openfe` is made available as a [conda-forge][] package, or [docker and singularity images][]. + +Please see our [installation instructions][] for details on how to install `openfe`. + +[Rocklin et al.]: https://doi.org/10.1063/1.4792251 +[Baumann et al.]: https://doi.org/10.1021/acs.jctc.3c00282 +[SepTop tutorial]: https://docs.openfree.energy/en/latest/tutorials/septop_tutorial.html +[SepTop user guide]: https://docs.openfree.energy/en/latest/guide/protocols/septop.html +[ABFE tutorial]: https://docs.openfree.energy/en/latest/tutorials/abfe_tutorial.html +[ABFE user guide entry]: https://docs.openfree.energy/en/latest/guide/protocols/absolutebinding.html +[Changelog]: https://docs.openfree.energy/en/latest/CHANGELOG.html +[NVIDIA multi-processing service]: https://developer.nvidia.com/blog/maximizing-openmm-molecular-dynamics-throughput-with-nvidia-multi-process-service/ +[docker and singularity images]: https://github.com/OpenFreeEnergy/openfe/pkgs/container/openfe +[conda-forge]: https://anaconda.org/conda-forge/openfe +[installation instructions]: https://docs.openfree.energy/en/latest/installation.html diff --git a/assets/images/per_benchmark_presentation.png b/assets/images/per_benchmark_presentation.png new file mode 100644 index 0000000..d0b9deb Binary files /dev/null and b/assets/images/per_benchmark_presentation.png differ