Hi,
we are trying to simulate ligand which is binding to the surface (exposed cavity) of a protein. The ligand topology was created from the antechamber and the complex was simulated using amber99sb using the gromacs. Upon simulation, we noticed that the ligand went away after 4 ns from the cavity. Fortunately, we know from the biochemcal/cellular experiments that ligand has target engagement. Now, we are having problems to depict it using MD. Can anyone suggest me any changes in restrain or parameter cut off to get the desired and unbiased results. please