Welcome to the new ACEMD3

ACEMD3 is a substantial development over ACEMD 2. Its new features include:

  • Improved performance
  • CPU support
  • Simplified input file
  • Improved barostat scheme

Installing ACEMD3

One can install the ACEMD3 with the command:

$ conda install acemd3 -c acellera -y

Running ACEMD3

ACEMD3 is run with the command acemd3. If you do not have a valid ACEMD Pro license the programme will run in Basic mode, with operation limited to the first GPU on your system.

If you have an ACEMD Pro license you may run on multiple GPUs with the --device flag, specifying the indices of the GPUs to use as an argument. To run in CPU only mode, use the argument --platform CPU. ACEMD3 will attempt to use all available CPU cores unless the environment variable NCPUS is set.

Input file changes

The ACEMD3 input file has been simplified. Where commands have been deprecated or changed name, ACEMD will print a warning explaining the change. The full command set is documented here.

TCL scripting is no longer supported in the input file. If you used TCL for applying restraints please read the documentation on applying restraints.

Discontinued Features

ACEMD3 does not contain support for:

  • Ensemble execution
  • Replica exchange
  • ACEMD Plugins
  • PLUMED 1


In case you encounter any issues with ACEMD3, please open an issue on our GitHub issue tracker if you are using the basic version of ACEMD3, or send an email to support@acellera.com if you are using the Pro version (>1GPU).