Parallelization of scientific applications remains a nontrivial task typically requiring some programmer assistance. In this study two similar parallelization tools, Pfortran and Cray's Co-Array Fortran, are discussed in the parallelization of GROMOS, a well known molecular dynamics package. It is shown that small number of extensions and intuitive application of Pfortran and Co-Array Fortran makes them efficient tool for parallelization of large scale applications.