Refactor minimize section

[rglez]

Instead of having one or several parameters in the config file dedicated to gather the CHARMM's topology/parameters files, let's create a folder where all these files reside.

Then, the only thing to specify in NUCLEAR config would be the path-to-this-dir and NUCLEAR will automatically recognize CHARMM's topologies & params using a specified file extension.

Any legal issue with distributing CHARMM's files?