# Release notes

## Unreleased

- mmCIF (`.cif`/`.bcif`) structure files can now be used for classical MD with OpenMM XML force fields, not only PDB. mmCIF preserves the full bond graph (including inter-residue bonds such as disulfides) and avoids PDB's 99,999-atom serial limit; it is the preferred structure format for the OpenMM XML route.
- `acemd.protocols.setup_equilibration` / `setup_production` now read the `system.yaml` handoff emitted by HTMD `openmm.build`, assembling the input file (structure, ordered parameters, box) automatically.

## 4.0.11 (2025-03-13)

- Support for OpenMM XML force field files (in combination with a PDB structure file).
- Added support for simulating triclinic boxes (truncated octahedra, rhombic dodecahedra).
- Removed `parmed` parsers; ACEMD now depends only on OpenMM. Fixes non-bonded CHARMM forces.

## 4.0.9 (2025-02-25)

- Improved protocol setup for CHARMM systems with multiple `prm` files.
- Fixed a bug where minimization was incorrectly performed on restarts.
- Added support for virtual sites (TIP4P water models).
- Massive speed-up for AceFF NNP simulations using CUDA graphs.
- Improved solvent handling — no more HMR on rigid water molecules.

## 4.0.1 (2024-12-05)

- Added Python setup for equilibration and production protocols.
- Fixed incorrect total charge of molecules in NNP/MM simulations.
- Documented warnings for NNP/MM on charged molecules.

## 4.0.0 (2024-12-01)

- Added support for NNP/MM simulations.
- Support for OpenMM 8+.
- Added `.yaml` and `.json` input files.
- Simplified the input-file options.
- New external-force description format.
- Added a basic Python API for executing simulations.

## 3.7.3 (2024-01-02)

- Fix license checking again.

## 3.7.2 (2023-06-07)

- Fix license checking.

## 3.7.1 (2023-04-14)

- Fix the reading of `parmfile` when it does not have an extension.
- Update MoleculeKit to fix an atom-selection issue when passing a list of integers to a float property.

## 3.7.0 (2023-03-27)

- Removed the device and virtualization limits for non-commercial users.
- Renamed the package and executable from `acemd3` to `acemd`. The old name still works for backward compatibility.

## 3.6.0 (2023-02-01)

- Updated to OpenMM 7.7.
- Replaced the old atom-selection code with MoleculeKit (fully compatible with HTMD).
- Improved the setup of the implicit solvent.
- Improved the configuration-file parser to give better error messages.
- Improved license checking and notifications.
- Improved documentation.
- Fixed the pinning of the CUDA Toolkit package so the latest compatible toolkit is installed.

## 3.5.1 (2022-09-30)

- Fix a licensing issue.

## 3.5.0 (2021-09-27)

- Updated to OpenMM 7.5.1 and PLUMED 2.7.1.
- Implemented support for IBM POWER9 (ppc64le) machines.
- Improved CHARMM parameter parser ([CHARMM-GUI](https://www.charmm-gui.org/)-generated files are parsed without errors).
- Implemented trajectory output of force and velocities (`trajForceFile` and `trajVelocityFile`).

## 3.4.1 (2021-04-21)

- Fix a dependency conflict with HTMD.

## 3.4.0 (2021-03-30)

- Updated to OpenMM 7.5.0 and PLUMED 2.7.0.
- Improved conda package; started using the conda-forge channel for dependencies.
- Refactored license checking and implemented the `--license` argument.
- Refactored the CMAP parameter parser and improved error messages.
- Switched to the standard PLUMED parser after it was fixed.

## 3.3.0 (2020-06-23)

- Implemented PLUMED support.
- Updated to OpenMM 7.4.2.
- Refactored the PRMTOP parser and improved error messages.
- Refactored the command-line parser and improved logging.

## 3.2.4 (2020-04-23)

- Fixed a bug in the CHARMM improper dihedrals.
- Fixed occasional crashes due to the Boost library.
- Fixed the documentation of `fbRefCoor`.

## 3.2.3 (2019-11-12)

- Fixed the DCD writer to include the size of a simulation box.
- Fixed overwriting/appending of trajectory files.
- Fixed `--ngpus` for more than 4 GPUs.

## 3.2.2 (2019-10-08)

- Fixed a corruption of the restart file.
- Fixed the name of the velocity file (`output.vel.coor` → `output.vel`).

## 3.2.1 (2019-09-20)

- Fixed the input-file reader to handle tabs as separators.

## 3.2.0 (2019-08-27)

- Implemented the multi-step integrator (`slowPeriod`).
- Implemented a DCD trajectory writer.
- Uniform input keywords.
- Limit restart to the same GPU.
- Implemented a trajectory writer for forces (`trajForceFile`).
- Implemented a keyword (`stepZero`) to enable output at step 0.
- Implemented the `--deterministic` argument.
- Refactored code and improved log messages.
- Improved testing.
- Updated performance benchmarks.
- Updated documentation.

## 3.1.2 (2019-06-04)

- Fixed a bug in the PDB reader again!

## 3.1.1 (2019-05-08)

- Fixed a bug in the PDB reader (only two characters of a residue name were read).

## 3.1.0 (2019-04-18)

- Optimised the code for performance.
- Implemented the `--precision` argument.
- Updated documentation.
- Added performance benchmarks.
- Fixed a bug in the setup of constraints.
- Fixed a bug in the minimizer to handle constraints correctly.

## 3.0.4 (2019-02-27)

- Fixed a code to report a correct version.

## 3.0.3 (2019-02-25)

- Improved the setup of group restraints.
- Improved energy conservation of the simulations.
- Enabled the minimizer to switch temporarily to CPU to avoid overflow.
- Extended the test suite of the code.
- Fixed a bug in the MD loop to run the exact number of steps.
- Fixed a bug in the minimizer to write the minimized positions.
- Fixed a bug in the minimizer to apply restraints.
- Fixed the restart of simulations.

## 3.0.2 (2018-03-28)

- Implemented the implicit-solvent model.
- Improved package building.
- Made the packages self-contained (no dependencies).

## 3.0.1 (2017-12-18)

- Fixed a bug in the license validation.

## 3.0.0 (2017-12-12)

- Initial release of the new ACEMD.