This manual is for the two simulation programs which have come to existence as a result of our ReaxFF realization efforts. Our initial efforts have led to the SerialReax program, which is a sequential implementation for ReaxFF. Serial- Reax has helped us in verifying the accuracy of our implementation in C against the original ReaxFF code which was developed in Fortran, such a task would be cumbersome in a parallel context. It has also served as a testbed for quickly implementing new algorithms and numerical techniques and benchmarking their effectiveness before we incorporated them into the parallel version. PuReMD (Purdue Reactive Molecular Dynamics) program is based on the sequential implemention, SerialReax, and highly efficient and scalable parallelization techniques. It inherits the excellent performance and small memory foot-print features of SerialReax and extends these desirable capabilities to systems of sizes that are of interest to computational scientists. For reasons described above, setting up a simulation and running it using PuReMD or SerialReax is quite similar to each other. Therefore in this manual, we take PuReMD as our basis and describe it first. In a following section, we describe the extras that come with SerialReax which we hope to incorporate into PuReMD in the near future.