It is relatively straightforward to set up a simulation of, say, a protein embedded in a lipid bilayer membrane or entry of a molecule into a membrane. However, it is considerably more difficult to set up a simulation involving diffusion through a membrane. Some good places to start include the websites for NAMD and CHARMM-GUI.

You can do that using biasing potential. Look for umbrella sampling.

Refer, GROMACS or NAMD tutorials on membrane simulations.

Hello, if you can. In my experience I have used the NAMD program, the CHARMM force field and for compounds I used CGenFF (https://cgenff.umaryland.edu).

Some articles that we have done in relation to the topic.

https://www.sciencedirect.com/science/article/pii/S0223523413003905

https://www.sciencedirect.com/science/article/pii/S0040403913021084

https://www.sciencedirect.com/science/article/pii/S0223523414001366