FAFNER2, which is a 3-D code adapted to the TJ-II helical axis stellarator from the original one developed by Lister at Max Planck IPP, simulates by Monte Carlo methods the neutral beam injection technology (a key heating method for most of the fusion experiments worldwide). To date, FAFNER2 has been usually run at CIEMAT by means of a batch mode on a shared memory computer with MIPS processors. This paper describes how the application has ben updated to employ MPI and run on standard Linux clusters. As in Grid infrastructures, not every site has MPI installed on their nodes; a serial version has also been developed, together with a Java Distributed Resource Management Application API program able to run FAFNER2 on distributed resource platforms, such as Grid infrastructures. In addition, and with new improvements in the code for maximizing its performance, the metascheduler GridWay has also been incorporated for maximizing the executions on the Grid. Scalability, fault tolerance, and correctness of the result have been proved employing a significant number of particles and nodes within a local cluster and the EGEE infrastructure.