[gmx-users] The non-protein system => .mdp file ?

[Chih-Ying Lin]

Hi
There are A_molecules, ion_Br , and water in the system and I will
make the .mdp files for the system. In the .mdp file, energygrps,
temperature coupling need to indicate the specified groups.
Could I just indicate these three kinds of groups, A_molecules,
ion_Br, and water ?


However, here is the idea of non-protein system from Tsjerk.
1.  " You'll have to work with an index file to make the distinction. "
      => how to group them?,
      => make  A_molecules and ion_Br as group_1
           make water as group_2 ?

2. "In some cases it may be better to use a single group "System",
which is a standard group (available without supplying an index
file)."
     => make A_molecule, ion_Br, and water as a group / a system?


3." In any case, DON'T couple each molecule separately."
      => what does this mean?

Thank you
Lin