GROMACs API vs sys.command

[mccrindlebrian]

We can execute GROMACs commands in two ways in python:

1. Using the GromacsWrapper, or
2. shell commands

We need to know which one is more suitable here (pros/cons). Things like

1. running in background threads/processes,
2. error handling,
3. code clarity and extensibility.

[schampoux]

• GMX seems to be the standard for running simulations. There is also an API built into the GMX package
• MDAnalysis package can be used to analyze results.

[schampoux]

GromacsWrapper:

• Known for its simplicity and ease of use.
• Follows a traditional command-line approach similar to running GROMACS commands directly.
• Can be easily integrated with python plotting libraries.

gmxapi:

• Provides the ability to interact with GROMACS functionalities using Python scripts.
• Can be easily integrated with python plotting libraries.