============= Release notes ============= 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 (i.e. truncated octahedra, rhombic dodecahedra) - Removed parmed parsers to only depend 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 - Updated documentation with warnings for NNP/MM simulations when simulating charged molecules 4.0.0 (2024-12-01) ------------------ - Added support for NNP/MM simulations - Support for latest OpenMM 8+ versions - Added support for ``.yaml`` and ``.json`` input files - Simplified the input file options - Added new external force description format - Added a basic Python API for executing simulations 3.7.3 (2024-01-02) ------------------ - Fix the licence checking again 3.7.2 (2023-06-07) ------------------ - Fix the licence checking 3.7.1 (2023-04-14) ------------------ - Fix the reading of ``parmfile`` when it does not have an extension. - Update MolekuleKit 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``. For backward compatibility, the old name still works. 3.6.0 (2023-02-01) ------------------ - Updated to OpenMM 7.7 - Replaced the old atom selection code with MoleculeKit to be fully compatible with HTMD - Improved the setup of the implicit solvent - Improved the configuration file parser to give better error messages - Improved licence checking and notifications - Improved documentation - Fixed the pinning of the CUDA Toolkit package so that the latest compatible toolkit is installed 3.5.1 (2022-09-30) ------------------ - Fix a licensing issue 3.5.0 (2021-09-27) ------------------ - Update to OpenMM 7.5.1 and PLUMED 2.7.1 - Implement support for IBM POWER9 (ppc64le) machines - Improve CHARMM parameter parser (`CHARMM-GUI `_-generated files are parsed without errors) - Implement the 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) ------------------ - Update to OpenMM 7.5.0 and PLUMED 2.7.0 - Improve Conda package and start using the conda-forge channel for dependencies - Refactor licence checking and implement ``--licence`` argument - Refactor the CMAP parameter parser and improve error messages - Switch to the standard PLUMED parser after its has been fixed 3.3.0 (2020-06-23) ------------------ - Implement PLUMED support and add a :ref:`tutorial ` - Update to OpenMM 7.4.2 - Refactor the PRMTOP parser and improve error messages - Refactor the command-line parser and improve logging 3.2.4 (2020-04-23) ------------------ - Fix a bug in the CHARMM improper dihedrals - Fix occational crashes due to the Boost library - Fix the documentation of ``fbRefCoor`` 3.2.3 (2019-11-12) ------------------ - Fix the DCD writer to include the size of a simulation box - Fix overwriting/appending of trajectory files - Fix ``--ngpus`` for more than 4 GPUPs 3.2.2 (2019-10-08) ------------------ - Fix a corruption of the restart file - Fix the name of the velocity file (``output.vel.coor`` --> ``output.vel``) 3.2.1 (2019-09-20) ------------------ - Fix the input file reader to handle tabs as a separators 3.2.0 (2019-08-27) ------------------ - Implement the multi-step integrator (``slowPeriod``) - Implement a DCD trajectory writer - Uniform input keywords - Limit restart to the same GPU - Implement a trajectory writer for forces (``trajForceFile``) - Implement a keyword (``stepZero``) to enable output at step 0 - Implement ``--deterministic`` argument - Refactor code and improve log messages - Improve testing - Update performance benchmarks - Update documentation 3.1.2 (2019-06-04) ------------------ - Fix a bug in the PDB reader again! 3.1.1 (2019-05-08) ------------------ - Fix a bug in the PDB reader (only two characters of a residue name were read) 3.1.0 (2019-04-18) ------------------ - Optimize the code for performance - Implement ``--precision`` argument - Update documentation - Add performance benchmarks - Fix a bug in the setup of constraints - Fix a bug in the minimizer to handle constraints correctly 3.0.4 (2019-02-27) ------------------ - Fix a code to report a correct version 3.0.3 (2019-02-25) ------------------ - Improve the setup of group restraints - Improve energy conservation of the simulations - Enable minimizer to switch temporally to CPU to avoid an overflow - Extend the test suite of the code - Fix a bug in the MD loop to run the exact number of steps - Fix a bug in the minimizer to write the minimized positions - Fix a bug in the minimizer to apply restraints - Fix the restart of simulations 3.0.2 (2018-03-28) ------------------ - Implement the implicit solvent model - Improve package building - Make the packages self-contained (i.e. no dependencies) 3.0.1 (2017-12-18) ------------------ - Fix a bug in the license validation 3.0.0 (2017-12-12) ------------------ - Initial release of the new *ACEMD*