CNS
CNS stands for "Crystallography and NMR System" and is an integrated and full-featured program for the determination and refinement of X-ray crystallographic and NMR structures.
Among its capabilities is simulated annealing molecular dynamics refinement.
There exists an inofficial parallelization (OpenMP) source code patch for CNS, distributed by kay dot diederichs at uni-konstanz dot de. The parallel version features (roughly) a 2-fold speedup on a 4-core machine for a typical simulated annelaing omit map run.
Consider also the more automated and user-friendly PHENIX which, although less complete, is under more active development.