We are pleased to announce the release of openfe version 1.11!
This release brings along some long-awaited features, notably support for membranes!
Please see below for some highlights and see the Changelog for more details.
New Features
Support for Protein-Membrane Systems
openfe can now perform simulations of proteins in membranes. These simulations require additional preparation: the user must supply a fully built, solvated, pre-equilibrated system, prepared with an external package. On the CLI, use the option --protein-membrane instead of --protein if you are providing this type of system, and see the new tutorial on RBFE Calculations of Protein-Membrane Sytems for guidance. You can find additional information in the User Guide.
Updated Default Settings for Improved Accuracy
By default, we now Lambda scale 1-4 interactions between core and dummy (i.e. unique in either end state) atoms in our hybrid topology protocol. In the past, such 1-4 interactions would be kept across the transformation. Our internal research shows that this modification yields a small, yet significant, improvement in the accuracy of relative binding free energy simulations.
Should you wish to toggle this feature, it can be controlled using the HybridTopologyProtocol alchemical settings turn_off_core_unique_exceptions parameter.
Installing openfe v1.11
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.