Release Notes, Version 2026.3.1

The following products have new versions for this release. Other packages are unchanged from the previous release.

Molecular Dynamics Floes Release Notes

v7.2.0 October 2026

General Notice

• This release introduces the new FE-NES for Binding Affinity Prediction Floe.

• This package is built using OpenEye-toolkits==2026.1.0, OpenEye-orionplatform==6.9.0, and OpenEye-Snowball==0.32.0.

• This release pins orionmdcore==2.7.2, which encapsulates the majority of code improvements, including:

  • Improvements to the energy minimization stage that ensure stable relaxation with enhanced handling of atomic clashes.

  • Support for OpenFF 2.2.1.

Major Changes

• We introduce the new FE-NES for Binding Affinity Prediction Floe that delivers a complete relative binding affinity prediction workflow in a single run, from equilibrium sampling and edge mapping to nonequilibrium switching calculations. Its redesigned submission interface and all-inclusive nature makes launching jobs easier.

• FE-NES is up to 2x faster than previous NES Floes.

• Scalability improvements now support up to eight concurrent jobs, each with 500 edges.

• A Trajectory Downloader Floe Report is available for MD Floes. MD trajectories are now stored in a single collection, making them easier to search and download and providing a more robust, streamlined workflow.

• FE-NES now uses a default bound-state limit of 250,000 atoms to help prevent unexpectedly large or costly calculations, or late-stage floe failures due to insufficient memory. This limit should only be increased when necessary and early validation with small test jobs is recommended. When removing this safety guardrail, a spot policy of prohibited is recommended on all bound-state MD cubes to avoid recurrent spot instance removal.

• Input of experimental affinity values as range values is now supported when affinity is provided through dataset column selection.

• The default force field for small molecules is now OpenFF 2.2.1.

• Promoted parameters have been renamed and default values for input/output datasets and files have been updated as shown in the table below.

Changes in promoted parameters and default input and output datasets and files.

Floe	OCLI Parameter Names		Default Output Names		Notes
	Old Version (v6.5.8)	New Version	Old Version (v6.5.8)	New Version
Analyze Protein-Ligand MD	--in	--md			Input
	--out	--eq_out	MD_Anlys	md_output_with_analysis
	--fail	--fail_out	failed_dataset	Failed Output for Analyze Protein-Ligand MD
Compare Experimental Affinity with End Point Analysis Results	--in	--equilibrium			Input
	--lig_exp_file	--exp			Input
Edge Mapper for RBFE Calculations	--mapper	--mapper_out	edge_mapper_output_dataset	edge_map
	--out_all	--all_out	all_possible_edges_dataset_output	all_possible_edges
Extend MD Simulations (Plain Molecular Dynamics)	--out	--md_out	md_output_dataset	md_output
	--recovery	--md_recovery_out	recovery_dataset	md_recovery
	--fail	--fail_out	failed_dataset	Failed Output for Extend MD Simulations
Plain Gromacs	--fail	--fail_out	failed_dataset	Failed Output for Plain Gromacs
Result Recovery for FE-NES (Nonequilibrium Switching Recovery)	--bound	--equilibrium			Input
	--DG	--affinity_out	binding_affinity_output_dataset	affinity_predictions
	--out	--nes_out	nes_output_dataset	relative_affinity_predictions
	--fail	--fail_out	failed_dataset	Failed Output for Result Recovery for FE-NES
Result Utilities for FE-NES (NES Result Utilities)	--bound	--equilibrium			Input
	--exptl	--exp			Input
	--DG	--affinity_out	binding_affinity_output_dataset	affinity_predictions
	--fail	--fail_out	failed_dataset	Failed Output for Result Utilities for FE-NES
Short Trajectory MD with Analysis	--out	--eq_out	MD_Bnd_Anlys	md_output_with_analysis
	--bnd_md_out		bnd_md_output_dataset		Removed
	--out_unb_analysis		MD_Unb_Anlys		Removed
	--fail	--fail_out	failed_dataset	Failed Output for Short Trajectory MD with Analysis
Solvate and Run MD	--out	--md_out	md_output_dataset	md_output
	--fail	--fail_out	failed_dataset	Failed Output for Solvate and Run MD

Floe Updates

• In the Edge Mapper for RBFE calculations Floe, the Write all possible edges parameter has been added to control whether all N*(N-1)/2 edges are written to the dataset (default: Off). In previous versions, the dataset was always written.

• In the Edge Mapper for RBFE calculations Floe, binary star map hubs can now contain commas and must be specified separately.

• In the FE-NES for Binding Affinity Prediction Floe, BAR overlap calculation is more stable (i.e., it reports a false overlap of 0.0 less often). A coding error has also been fixed that previously led to incorrect BAR overlap values. New, correct values are typically smaller. This only affected BAR overlap, and did not affect \(\Delta\Delta G\) or \(\Delta G\) binding affinity estimates.

• Because FE-NES for Binding Affinity Prediction is comprehensive, the Equilibration and Nonequilibrium Switching, Nonequilibrium Switching, and Ligand Bound and Unbound Equilibration for NES Floes have been removed.

• The Plain Molecular Dynamics Floe has been renamed to Extend MD Simulations to better describe the purpose of the floe.

• The NES Result Utilities Floe has been renamed to Result Utilities for FE-NES.

• The Nonequilibrium Switching Recovery Floe has been renamed to Result Recovery for FE-NES.

Molecular Dynamics Core Package Release Notes

v2.7.2 October 2026

General Notice

• This package is built using openeye-orionplatform >=5.1.1, <6.10.0, openeye-snowball >=0.26.0, openeye-toolkits >=2024.1.1, openff-toolkit >=0.17.0, <0.18, and parmed >=4.3.0, <5.

• Performance improvements and minor bug fixes have been made to support MD Affinity Floes v7.2.0.

Updates

• MD trajectories are now uploaded as shards instead of trajectory files.

• The energy minimization stage has been improved to ensure stable relaxation and better handling of atomic clashes.

• Support has been added for OpenFF 2.2.1, which is now the default force field for ligand components.