Flexible bodies of arbitrary shape
MW can simulate objects with arbitary shape using an approximation that discretizes a shape into connected particles. Such an object does not need to be rigid bodies. They can interact with each other, as well as with atoms and molecules represented by balls and sticks. They can vibrate and their shapes can distort. To learn more about how these objects are constructed, see this reference: C. Xie, Molecular dynamics simulations beyond the Lennard-Jones particles, unpublished. (PDF)