[obasekia]

Good day all, i have a question about steered MD simulation implemented in genesis, if for example i want to calculate the dissociation of Ligand from my substrate , can i use steered MD?

[ckobayashi]

Hello,

This is a difficult question to answer in general. I can just say that with atdyn you can change a distance reference in the Steered MD (SMD), but with spdyn we can only change a rmsd one. But to be honest, I don’t know if we can investigate the dissociation of ligand just by changing DISTANCE in the SMD.

 

Sincerely yours,

Kobayashi