Provided that you apply the right and valid force field for each system, you can simulate properties that closely could be related to the experimental results. Application of NBO charges for the ligands could lead to better results. You should also be aware of many simulation tricks.

Dear Dr.Mohammed,

Thanks a lot for your answer.

My first host is a cyclodextrin (Drug carrier), the second host is Albumin. I would like to see if the drug will leave the cyclodextrin carrier easily and go to bind the Albumin. I want to compare the PMF between two different drugs. I know that I may simulate each system alone and calculate PMF with respect to the dissociation from cyclodextrin and the association to Albumin, but, do you think it is reasonable to do the two simulations simultaneously and trace the PMF to see which is easier to happen. I have looked at the literature and i did not find something similar, perhaps I am missing something here. Do you have any suggestions for such simulations?. Do you see any preference for steered MD over adaptive biasing force MD to do such calculations. Do you have any preference for one software to another, I am comfortable with AMBER but also have quiet experience with NAMD and GROMACS.

Thanks in advance

Marawan