Biobb GROMACS changelog
What’s new in version 5.2.1?
Changes
[UPDATE] Update to biobb_common 5.2.2
What’s new in version 5.2.0?
Changes
[UPDATE] Update to biobb_common 5.2.0
What’s new in version 5.1.2?
Changes
What’s new in version 5.1.1?
Changes
[UPDATE] Update gromacs version to 2025.2
FIX: Fixed make_ndx stdin bug
What’s new in version 5.1.0?
Changes
FEATURE: Append_ligand: take into account [ atomtype ] section when including itp files
FIX: Avoid defining variable twice
FIX: ndx2resttop: fixed index_dic creation
FEATURE: ndx2resttop: added custom posres name
FIX: Take into account single chain situations with just a .top file
FIX: ndx2resttop: clean mdp keywords before merging to avoid duplicates
FEATURE: pdb2gmx: extend the interactive choice of protonation state for all titratable residues
FEATURE: pdb2gmx: support multi chain PDBs when titrating
FIX: genion: fix default concentration
[UPDATE] Update gromacs version to 2024.5
What’s new in version 5.0.0?
Changes
CI/CD: Update biobb_common version.
Typing: Update typing from python 3.8 style to python 3.9
CI/CD: Adding global properties to test yaml configuration
CI/CD: Update GA test workflow to Python >3.9
DOCS: Updating to Python 3.9
CI/CD: Update .gitignore to include the new file extensions to ignore
CI/CD: Change test conf.yml to adapt to new settings configuration
CI/CD: Adding the py.typed
[FIX] Adding execution permissions to append_ligand
[UPDATE] Adding sandbox_path property to the json schemas
[FEATURE] New sandbox_path property
[CI/CD] Update grompp reference files and GA WF
What’s new in version 4.2.0?
Changes
[DOCS] Adding fair software badge and GA
[FIX] Fixing type hints problems
[FIX] Type Hints Errors
[DOCS] Adding CITATION.cff in paths-ignore
[DOCS] Howfairis checker
[DOCS] Adding CITATION.cff and badges to the readme
[CI/CD] Adding Castiel Gitlab push sync github Action
What’s new in version 4.1.1?
New features
Check for GROMACS version now raises a warning instead of an Exception.
What’s new in version 4.1.0?
New features
TRR file output is now optional in mdrun.
Extended functionality and usage of gmx_check.
What’s new in version 4.0.0?
New features
New biobb_common new properties and features there.
New GROMACS default version 2022.4
What’s new in version 3.9.0?
New features
All inputs/outputs are checked for correct file format, extension and type (general)
What’s new in version 3.8.1?
New features
New Trjcat block (general)
What’s new in version 3.8.0?
In version 3.8.0 the default GROMACS version will be v2022.2
New features
Update to biobb_common 3.8.1 (general)
What’s new in version 3.7.1?
Bug fixes
Problem with Gmx version check (mdrun) #48
What’s new in version 3.7.0?
In version 3.7.0 the dependency biobb_common has been updated to 3.7.0 version.
New features
Update to biobb_common 3.7.0 (general)
What’s new in version 3.6.0?
In version 3.6.0 Python has been updated to version 3.7 and Biopython to version 1.79. Big changes in the documentation style and content. Finally a new conda installation recipe has been introduced.
New features
Update to Python 3.7 (general)
Update to Biopython 1.79 (general)
New conda installer (installation)
Adding type hinting for easier usage (API)
Deprecating os.path in favour of pathlib.path (modules)
New command line documentation (documentation)
Bug fixes
Replace container Quay.io badge (documentation)
Remove unused system and step arguments from command line causing execution errors (cli) #9
Other changes
New documentation styles (documentation) #8