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-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.