I'm proposing this change because currently the chosen groups in the .mdp settings of sim.xml (Protein and Non-Protein) will only work for a system with peptides in it. Given the diversity of the chemical systems that can be simulated in GROMACS, and thus the versatility that could be extended to users of galaxy, I recommend changing these groups to "non-Water and Water" in order for the simulations to run across many different chemical species.
In general, one is trying to thermocouple the system here. This can be achieved by using a single coupling group (System), or if we choose to use two for more accuracy, then what we should be coupling are "solutes and non-solutes". The easiest way to achieve this, using the automatically indexed groups in any water-solvated system, is "non-Water Water".
I'm proposing this change because currently the chosen groups in the .mdp settings of sim.xml (Protein and Non-Protein) will only work for a system with peptides in it. Given the diversity of the chemical systems that can be simulated in GROMACS, and thus the versatility that could be extended to users of galaxy, I recommend changing these groups to "non-Water and Water" in order for the simulations to run across many different chemical species.
In general, one is trying to thermocouple the system here. This can be achieved by using a single coupling group (System), or if we choose to use two for more accuracy, then what we should be coupling are "solutes and non-solutes". The easiest way to achieve this, using the automatically indexed groups in any water-solvated system, is "non-Water Water".