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if molecule A be in charmm force field and molecule B be in Amber
force filed,How could I simulate these molecules with two different
special bonds?
you should not do that. one key element of force fields
is that they have carefully balanced interactions, e.g.
between charges and lennard-jones interactions and
between solute and solvent. now if you mix force fields,
you are breaking this balance. in particular, CHARMM
and Amber have different water potentials and use different
methods to determine the charge distribution. that will
lead to inconsistencies, which are likely to compromise
the validity of your simulations.
you will have to switch to either charmm or amber
for _all_ molecules.
axel.