This paper analyzes in detail the difficulties and issues that must be faced when running MPI (Message Passing Interface) applications over non-dedicated infrastructures. Alternatives to overcome these issues on a specific opportunistic infrastructure, called UnaCloud, are presented. We designed and implemented a UnaCloud extension to allow automatic recovery of the execution of MPI applications. This extension will provide new opportunities for research groups, allowing researchers to run MPI applications with a minimum overhead and at a low cost. We tested our implementation running a large application for several hours: Gromacs MPI, a molecular dynamic application that uses MPI to predict and redefine the tertiary structure of a particular protein. Our results show that running such an application is indeed possible, even if the underlying infrastructure exhibits high volatility. This provides a setting to introduce UnaCloud as an opportunistic platform that can be used to run Bag of Tasks (BoT) and MPI applications.