Can elastic elements (ligaments, cartilage..) be modelled?
You can actually specify ligaments and other (passive element) forces that depend on position and velocity (in general springs and dampers with almost any explicit expression you can come up with). In particular, we have a ligament object class which is specially designed for ligament, but in general it is nothing else than an applied force. The downside is that the ligament forces cannot be a function of the muscle forces in this way, since they merely enters the inverse dynamics solution as applied forces. We hope to resolve this problem in a future version. One could currently model ligaments as simple muscles. This has, as far a I know, been done in some studies in the literature.