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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 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

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