Special-purpose computing hardware can provide significantly better performance and power efficiency for certain applications than general-purpose processors. Even within a single application area, however, a special-purpose machine can be far more valuable if it is capable of efficiently supporting a number of different computational methods that, taken together, expand the machine's functionality and range of applicability. We have previously described a massively parallel special-purpose supercomputer, called Anton, and have shown that it executes traditional molecular dynamics simulations orders of magnitude faster than the previous state of the art. Here, we describe how we extended Anton's software to support a more diverse set of methods, allowing scientists to simulate a broader class of biological phenomena at extremely high speeds. Key elements of our approach, which exploits Anton's tightly integrated hardwired pipelines and programmable cores, are applicable to the hardware and software design of various other specialized or heterogeneous parallel computing platforms.