Allow the ability to add arbitrary control parameters to mdrun

[IAlibay]

Currently it probably will pick up GPUs, but not very well, nor will it play well with ntomp flags.

[RiesBen]

ntomp can be modified in the current version.
GPUs however are a headache to me. I allow to pass a gmx_kernel and to modify the simulation execution this way.
(see https://github.com/bigginlab/ABFE_workflow/blob/894b9b11ef900bc8d571fbaf325f7bd610e5e43c/abfe/template/gmx_submit_kernels/def_cpu_job.sh
and
https://github.com/bigginlab/ABFE_workflow/blob/894b9b11ef900bc8d571fbaf325f7bd610e5e43c/abfe/template/gmx_submit_kernels/def_cpu_job_cont.sh
)

[IAlibay]

Can we not define -nb and -pme in the same way?