# Biobb GROMACS changelog ## What's new in version [5.2.1](https://github.com/bioexcel/biobb_amber/releases/tag/v5.2.1)? ### Changes * [UPDATE] Update to biobb_common 5.2.2 ## What's new in version [5.2.0](https://github.com/bioexcel/biobb_amber/releases/tag/v5.2.0)? ### Changes * [UPDATE] Update to biobb_common 5.2.0 ## What's new in version [5.1.2](https://github.com/bioexcel/biobb_gromacs/releases/tag/v5.1.2)? ### Changes * [UPDATE](https://github.com/bioexcel/biobb_gromacs/commit/37ecf702130ee32559f43838b2886032cf831892) Add npappend to mdrun * [FATURE](https://github.com/bioexcel/biobb_gromacs/commit/e44c7193b275810992b12948cbc1c50c680e5b63) Add convert.tpr block * [UPDATE] Update biobb_common to 5.1.1 ## What's new in version [5.1.1](https://github.com/bioexcel/biobb_gromacs/releases/tag/v5.1.1)? ### Changes * [UPDATE] Update gromacs version to 2025.2 * [FIX](https://github.com/bioexcel/biobb_gromacs/commit/5c429081aeaae513b61bc273aec2e6c67ff15dce): Fixed make_ndx stdin bug ## What's new in version [5.1.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v5.1.0)? ### Changes * [FEATURE](https://github.com/bioexcel/biobb_gromacs/commit/acf09cbc4d4fa5dc5f2db8dee29434e313601beb): Append_ligand: take into account [ atomtype ] section when including itp files * [FIX](https://github.com/bioexcel/biobb_gromacs/commit/aa6afa4b4346f800d00b5d86d0ba7d342ed74cdc): Avoid defining variable twice * [FIX](https://github.com/bioexcel/biobb_gromacs/commit/db9a0a62bc38214e5aaeed9b61d1eafb6ad1e8f3): ndx2resttop: fixed index_dic creation * [FEATURE](https://github.com/bioexcel/biobb_gromacs/commit/c3e9cd901bae89f087e8f5efdfaea8b981533b45): ndx2resttop: added custom posres name * [FIX](https://github.com/bioexcel/biobb_gromacs/commit/1bcc746b60b6555cc244c086ab3483797e5c52bf): Take into account single chain situations with just a .top file * [FIX](https://github.com/bioexcel/biobb_gromacs/commit/60f8d26e9495b41cd49797ee33ea5e8c59edfe53): ndx2resttop: clean mdp keywords before merging to avoid duplicates * [FEATURE](https://github.com/bioexcel/biobb_gromacs/commit/4681ed7c380c2f83970da1280866c8eb414945b7): pdb2gmx: extend the interactive choice of protonation state for all titratable residues * [FEATURE](https://github.com/bioexcel/biobb_gromacs/commit/your_commit_hash): pdb2gmx: support multi chain PDBs when titrating * [FIX](https://github.com/bioexcel/biobb_gromacs/commit/762b3a6fcad3b2ad3238212c1190470ce2245b80): genion: fix default concentration * [UPDATE] Update gromacs version to 2024.5 ## What's new in version [5.0.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v5.0.0)? ### Changes * [CI/CD](env.yaml): Update biobb_common version. * [Typing](ALL): Update typing from python 3.8 style to python 3.9 * [CI/CD](conf.yml): Adding global properties to test yaml configuration * [CI/CD](linting_and_testing.yaml): Update GA test workflow to Python >3.9 * [DOCS](.readthedocs.yaml): Updating to Python 3.9 * [CI/CD](GITIGNORE): Update .gitignore to include the new file extensions to ignore * [CI/CD](conf.yml): Change test conf.yml to adapt to new settings configuration * [CI/CD](py.typed): 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](https://github.com/bioexcel/biobb_gromacs/releases/tag/v4.2.0)? ### 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](https://github.com/bioexcel/biobb_gromacs/releases/tag/v4.1.1)? ### New features * Check for GROMACS version now raises a warning instead of an Exception. ## What's new in version [4.1.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v4.1.0)? ### 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](https://github.com/bioexcel/biobb_gromacs/releases/tag/v4.0.0)? ### New features * New biobb_common new properties and features there. * New GROMACS default version 2022.4 ## What's new in version [3.9.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v3.9.0)? ### New features * All inputs/outputs are checked for correct file format, extension and type (general) ## What's new in version [3.8.1](https://github.com/bioexcel/biobb_gromacs/releases/tag/v3.8.1)? ### New features * New Trjcat block (general) ## What's new in version [3.8.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v3.8.0)? 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](https://github.com/bioexcel/biobb_gromacs/releases/tag/v3.7.1)? ### Bug fixes * Problem with Gmx version check (mdrun) [#48](https://github.com/bioexcel/biobb_gromacs/issues/48) ## What's new in version [3.7.0](https://github.com/bioexcel/biobb_gromacs/releases/tag/v3.7.0)? 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](https://github.com/bioexcel/biobb_gromacs/releases/tag/v3.6.0)? 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](https://github.com/bioexcel/biobb_model/issues/9) ### Other changes * New documentation styles (documentation) [#8](https://github.com/bioexcel/biobb_model/issues/8)