GROMACS data

Our newest addition to AMEP is the possibilty to read GROMACS simulation data. GROMACS (Groningen Machine for Chemical Simulations) is commonly used for molecular dynamics simulations. Although not active, the dynamics and behaviour on a molecular level can give fascinating new insights into the whole realm of soft matter.

We use the python package chemfiles (https://chemfiles.org/) to read the binary trajectory and topology/run input files.

Note

Currently, chemfiles does not read forces from trajectory files. chemfiles/chemfiles#496

As soon as this is supported by chemfiles this feature will be included AMEP.

AMEP also includes a basic mechanism to identify molecules, making molecule-based analysis more accessible than using GROMACS index files.