Customizing the gmx mdrun Parameters

[ErikZhang-9762]

Is your feature request related to a problem? Please describe. When using gromacs, define some parameters to speed up the simulation

Describe the solution you'd like I would like to be able to add the following customized parameters to the gromacs command afterwards for example：

gmx mdrun -v -deffnm gromacs  -ntmpi 1 -ntomp 28 -gpu_id 0 -pin on -pinstride 1 -pinoffset 0 -update gpu -bonded gpu

Describe alternatives you've considered None

Additional context None

Is there currently any way to do this?

[lohedges]

Yes, there are multiple ways to do this. You can either use the extra_args kwarg when creating your process object, or the setArg and setArgs methods on an existing process. The command-line arguments take the form of an ordered dictionary. You can use getArgs on an existing process to see how this is formatted. This is all documented in the API docs, e.g. here

https://biosimspace.openbiosim.org/api/generated/BioSimSpace.Process.Gromacs.html

[lohedges]

Closing since the question has been answered.