Molecular Dynamics Core Package

v2.6.1 April 2026

This package is built using openeye-orionplatform >=5.1.1, <7, openeye-snowball >=0.26.0, openeye-toolkits >=2024.1.1, openff-toolkit >=0.17.0, <0.18, and parmed >=4.3.0, <5.

Support has been added for Python 3.10+.
The package has been updated to use ParmEd 4.3.0.
Compatibility has been added for NumPy 2 (<=2.2.6 due to constraints from ParmEd).
Compatibility has been added for the latest versions of MDTraj.
Support has been added for OpenMM up to 8.2 (was 8.1).
AmberTools have been validated and upgraded to version 24.8. This update also raises GAFF2 from version 2.11 to 2.2.20. Although this change is not explicitly noted in the AmberTools changelog, the Amber developers recommend using the latest GAFF2 release over the earlier version (see this email exchange for details). Set ligand_forcefield on ForceFieldCube to "Gaff_2.2.20" if you wish to use GAFF2. The original "Gaff_2.11" option is obsolete.

A new option called orient_solute has been added to the Solvation Cube to control whether the solute should be oriented such that its principal axes align with the coordinate axes. In combination with the rectangular box shape, this option can be used to minimize box sizes and therefore reduce the simulation cost.
If you wish to use GAFF2, set ligand_forcefield on the Force Field Cube to "Gaff_2.2.20". The original "Gaff_2.11" option is obsolete.