Suggestions for simulating transport through membranes with Molecular Dynamics (MD) and Monte Carlo (MC)?
I always find AMBER to be the most streamlined for conducting MD, however it (as well as CHARMM) are proprietary.  Note that both are Langevin dynamics based, whereas LAMMPS is brownian dynamics.  

That being said, an MD simulation is only as good as the parameters for the force field; the engine is of no matter (unless we're discussing speed).  Basically, I would use a QM program (Gaussian is my goto, but nwchem or psi4 are excellent open source options) to optimize the geometry of the membrane.  Because this is rather heavy, you'd most likely be best to go with a semi-empircal method as ab-initio could take weeks (depending on your computational power).  Once optimized, use the QM software to derive force constants as well as ESP charges (partial charges) for each atom.  Take this data, and parameterize a force field with it (I'm partial to using the Amber FF's...google GAFF or FF99SB... Theres a paper out there from Cornell, Merz, et. al. that should give you insight). 

I hope this helps give you an idea of what you're looking at for a respectable MD simulation.