There has been some recent interest/questions among group members in simulating membrane proteins, and when it comes to using the CHARMM force field, I thought I'd point to this useful resource for anyone who might be interested: the 'membrane protein tutorial' at http://www.ks.uiuc.edu/Training/Tutorials/, which is a very useful tutorial on how to prepare your lipid+protein system.
One thing that is worth noting is that the above tutorial hasn't been updated for the latest CHARMM lipid force field, C36. If you'd like to use this new FF, you'll need vmd-1.9, and specify the C36 topology file when calling the membrane plugin. More info has been added to the group wiki: https://wiki.mccammon.ucsd.edu/index.php/MolecularDynamics
Since the C36 FF is a fairly recent update, if your simulations started with the older C27 FF (like some of my simulations), it's probably not a bad idea to be consistent within the same study, as the two FF will likely co-exist in the literature for a while. But if you're starting a brand new system/simulation, you might as well start with the new C36 FF, which I imagine will gradually replace C27.