The invasive Run-time Support System (iRTSS) is a run-time system that supports the invasive MPI API (iMPI). iMPI extends the functionality of the standard MPI such that applications using it can be malleable (i.e., change their resources at runtime). During the thesis we ported miniMD, a C++ molecular symulation code, to the iRTSS. miniMD is a simplifaction of the well-known LAMMPS application. As part of this thesis we developoed a TCP/IP communication scheme to gather the results of the simulation, which runs directly on the bare metal, on a second Linux machine. miniMD was also extended with new simulation scenarios.