So you want to have concurency between the two ligands? Why shouldn't it work?

I have used NAD and Inhibitor simulation using Gromacs. Find out if your forcefield contains the NAD parameters. Otherwise you need to add parameters of your ligands to  .conf and .topol files separately. Yes its possible to simulate a protein with two ligands using gromacs.

I have run an antibiotic-induced protein complex dissociation in AMBER. It went well. As Raj said, the only trick is to have set properly  the two ligands parameters.

Please provide detail methodology and research article on multi ligand simulation