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
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