Hello,
I want to run MD with GAFF for a conformational polymorphic crystal with many conformations. Should I parametrized for one conformation and use the same for other conformations or Is there any correct way to parameterized GAFF in case of multiple conformations.
Assuming it’s a molecular crystal, you should parametrize the components in the gas phase to avoid energy barriers due to sterical clashes with neighbours. Typically, the key parameters are dihedral angle potentials and atomic charges.
Once your force field has been optimised, you must use it to compute the relative energy of the various polymorphs. Otherwise, you cannot rank them.