[gmx-users] Problem in protein ligand interaction

[Gonzalez Fernandez, Cristina]

Dear Gromacs users,


I'm trying to simulate a protein-lipid interaction. Analyzing the simulation, it seems that the lipid does't have enough driving force to reach the binding pocket, since van der Waals forces move the lipind towards the binding pocket whereas electrostatics move the lipid in the opposite direction. How could I achieve that the lipid reaches the protein binding site? Could I include some distance restraints that help the lipid to move to the binding pocket and then switch them off or this idea would lead to unreliabe results?


Thank you in advance for all your help!


Regards,


Cristina