Define MD engine run command in Python

[mimischi]

A user currently writes the whole run command in their job script by hand. We just replace a few variables.

MDBenchmark/mdbenchmark/templates/draco

Lines 35 to 40 in 4f3bb5f

	# Run {{ module }} for {{ time }} minutes
	{%- if mdengine == "gromacs" %}
	srun gmx_mpi mdrun -v -maxh {{ time / 60 }} -deffnm {{ name }}
	{%- elif mdengine == "namd" %}
	srun namd2 {{ name }}.namd
	{%- endif %}

It would probably be of greater use to generate this whole line in Python and just replace one variable, e.g., {{ hpc_command }} in the job script. This would help with later features like parameterization of HPC/MD engine specific settings. Also we would not need all those if-clauses ({%- if mdengine == "gromacs" %}), when we add more MD engines.

CC @kain88-de @MSiggel: I would suggest to push this feature to the future (3.0?), because we would be massively changing the user-facing interface again. I am not sure if we can fully flesh out the details and finish it before we release 2.0. Or maybe we introduce it in 2.x and deprecate old variables in 3.0 (if we need to deprecate them at all).