[gmx-users] restraints between two molecules

[lq z]

Dear GMXers,

I can apply harmonic bond, angle, and dihedral restraints between two
molecules (3 atoms on one, and one atom on the other one). If yes, how to
set it up in the topology file?

Question 2: Can I apply distance restraint between mass center of some
atoms in one molecule and ONE ATOM in the other molecule?

Question 3: Can those restraints be lambda (in alchemical free energy
simulation) dependent?

You may have known what I'm trying to do: Change one molecule to dummy, so
I need restrain it at dummy state while no restraint is wanted at real
state.

Thanks,
Luke
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