[gmx-users] Define custom moltype for free energy calculations

[Tom Newport]

To give some background, I would like to be able to perform free energy
calculations using a variety of different fairly complex selections to
specify which bits of the system to turn on or off. These may include
several proteins and several different ligands. There are other proteins
and ligands which I do not want to include. This is for coarse-grained
(martini) simulation of proteins and lipids, although I assume that doesn't
make a difference.

So, how is a moltype specified in GROMACS, and what is the least messy way
of adding several molecules to one moltype? (or can this be specified more
easily, say through using an index file?)

Any help greatly appreciated!

Tom