modified sim.xml and macros.xml to allow for system thermocoupling and option to start velocities at NVT

[thepineapplepirate]

Now being able to choose to couple the entire system, users will no longer be limited to simulations of peptides. Before this, the default option was a dual coupling setup where it was set to "Protein Non-Protein". This would cause a failure any time someone simulated non-peptide systems. The new option to couple the whole system will allow users to virtually use any .gro file. Changes were made to both the sim.xml file and the macros.xml file.

Additionally, the option was added to add starting velocities in an NVT simulation. I made it an option via conditionals for this rather than having it hard coded, even though, in practice one should always assign starting velocities at NVT (the system needs to start with some kinetic energy). Cheers!

[simonbray]

Thanks @thepineapplepirate!

[thepineapplepirate]

Thanks Simon!