🗒️ Changelog

🗒️ Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[0.16.3] - 2026.05.10#

Fixed#

  • #52: Mismatch between tests and package.

  • Update docs.

  • preparation.system_builder.system_combiner. Use slicing instead deep copy so the Structure class initialize properly avoiding errors such as AttributeError: 'GromacsTopologyFile' object has no attribute 'symmetry'.

Added#

  • Keyword cofactor_selection, this is a GMX selection for better control of the definition of complex cofactors given via .gro/.top files. For example: “resname GDP or resname GTP or resname MG”. This is used for the definition of the groups in the thermostat for membrane systems, This is only relevant for membrane systems. For soluble systems everything is treated as a single group.

  • solv_d, solv_bt (d and bt flags of gmx editconf), solv_rmin, and solv_ion_conc (rmin and conc flags of gmx genion) to bindflow.runners.calculate(). Now there is more room to control the solvation step.

Changed#

  • Tests are part of the wheel, pytest --pyargs bindflow.tests is used for testing.

  • The box type for soluble complex and the ligand simulation was hard coded to octahedron, now it is customizable with solv_bt, but the default value is the more efficient dodecahedron box.

0.15.1 - 2026.03.17#

Added#

  • CI/CD for PyPI deployment

  • Check for gmx version

Changed#

  • Update documentation, tutorials and installation

  • Improve code styling

  • Use always 1 bar instead 1.01325 for membrane simulations during equilibration

Fixed#

  • Better logging

  • Move to new setuptools and update versioning

  • Exclude pme flag during equilibration

  • Pass gmx dependencies during solvation

Removed#

  • MDP options from bonded and coul windows as there are not being used. Those flags are only relevant when either Lennard-Jones or Coulomb interaction are decoupled. In our case for coul they also irrelevant as the options are applied only if sc-coul = yes, which by default is no. Check the GROMACS docs for more info on these MDP options.

sc-alpha                 = 0.5
sc-power                 = 1
sc-sigma                 = 0.3

  • "MDRestraintsGenerator @ git+https://github.com/ale94mleon/MDRestraintsGenerator.git@dev" dependency from pyproject.toml as it is not accepted by PyPi. This dependency is built during the conda environment step anyway.

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