Added prefixes for running KIMMDY on HPC Clusters that require srun/mpirun for gromacs binaries #517
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…r gmx_mpi on mpcdf. grompp_prefix will now be used (if not None) at these non-mdrun gmx calls. Added new parameters to yaml schema. Improved handling of new parameters to avoid additional spaces if None.
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Added new config parameters in yaml-schema and incorporated them into functions
get_gmx_dir(),_run_md()and_validate(). Could not yet be validated if it runs WITHOUT defining the prefixes. This would be necessary before merging. When not defined, the prefix defaults are "" and no spaces are added to gromacs commands.