5. PLUMED interface

HyMD is interfaced with PLUMED <https://www.plumed.org/> for simulations using enhanced sampling or free-energy methods. To use the interface, the Python package of PLUMED must be installed, and the user must provide a working PLUMED_KERNEL by setting this environment variable to the kernel path. In the current version, only simulations using a single replica are supported.

Warning

PLUMED versions prior to 2.8.1 did not have a working Python interface with MPI. Therefore, you must use PLUMED 2.8.1 or greater when installing the PLUMED library in Python. Older versions for the kernel are supported if the Python interface was correctly installed with version 2.8.1.

5.1. Running simulations using PLUMED

To run your simulations using PLUMED you must first set the environment variable PLUMED_KERNEL and then call HyMD with the --plumed option, passing the PLUMED input file to HyMD. Optionally, you can also set the output file name with the --plumed-outfile option (the default it plumed.out).

If your PLUMED input (see the PLUMED manual <> for details) is called, e.g., plumed_input.dat, you can run a simulation using the PLUMED interface with:

python3 -m hymd ideal_chain.toml ideal_chain.HDF5 --disable-field --plumed plumed_input.dat