Release 1.7 blog post

_posts/2025-10-23-release-v1.7.md

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+---
+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][]
+
+<center><img src="/assets/images/per_benchmark_presentation.png" alt="average cost of a ligand pair alchemical cycle over the JACS set." style="width:550px;"/></center>
+
+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