[gmx-users] Python API Documentation question

[Marko Petrovic]

Hello

As I'm quite new to both gromacs in and of itself and the python API I'm struggling a bit figuring out how to go about getting simulations running using the API. I've managed to write a Python script creating and running shell command line commands to run through the Lysozyme tutorial, but that totally circumvents the API. The API has a function "commandline_operation" which I believe should also be usable for this, unfortunately I can't say I'm totally clear on the nomenclature used in the documentation so I'm unsure of what or where I go wrong.
For example the executable parameter and arguments parameter in "gmx grompp"... is gmx the executable withh grompp a parameter or grompp the executable and the rest of the line parameters?
And input_files and output_files, are they meant to be declared in those parameters only, in arguments only or both, and do flag keys need the dash prefix?

I will be very thankful for any help anyone can give regarding this.

With Regards
Marko Petrovic
Educator
Computational Science and Technology
School of Electrical Engineering and Computer Science
KTH Royal Institute of Technology