Hi,

I think the best way is you to follow GROMACS manual and the original publication:

https://manual.gromacs.org/documentation/2018/user-guide/mdp-options.html#computational-electrophysiology

https://manual.gromacs.org/documentation/2018/manual-2018.pdf

Article Computational Electrophysiology: The Molecular Dynamics of I...

All information you require is there and it is not difficult to assemble a system to do that. BUT you will require a lot of computational power because, usually, you must have two protein+membrane systems and a very large system (> 500.000 atoms) with explicit waters.

Unless you have such computational capability, I advise you to use other techniques (e.g. umbrella sampling, metadynamics).

@Ricardo J Ferreira could you please provide the tutorial for metadynamics simulation in gromacs?

Also how can I use umbrella sampling to measure conductance in an ion channel