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

[chris.neale at utoronto.ca]

The main point is that you don't want to have a temperature coupling  
group that does not contain many atoms. Ions are usually grouped with  
water. Therefore, without any more information I would suggest the  
following:

1) Assuming A_molecules are >> 100 atoms:
    - 2 groups: i) A_molecules, and ii) ion_Br_&_water

2) If A_molecules are smalle:
    - 1 group: i) System

Of course there are exceptions to this, but if you are doing a  
straightforward simulation then this should be fine.

Chris.

-- original message --


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