Desmond is probably the best MD engine out there, especially if you have an InfiniBand cluster. In addition to Desmond itself, it comes with a bunch of goodies such as viparr and msys, which are top-notch modeling tools. Desmond build problem is solved by using SCONS, a python-based build tool. To my surprise the build process went super-smooth! That said, I don't have the necessary sequence of "sudo apt-get install packageA packageB". Please checkout the share/ to get a feel for what Ubuntu packages you might need; frequently a '-dev' package will be needed. Here is what i did The build/ config is shown below Then testing the build to check if the random number is generating the expected random number ;) Test restoring the checkpoint capacity; the files 'dhfr.eneseq' and 'dhfr.eneseq.original' should be identical. Finally, test the parallel part. Here there should be a good match of energies dhfr.eneseq.2 with the previous two runs: