Constant pH Method: Capturing Proton Movements in Molecular Dynamic Simulations
Constant pH dynamics is a simulation procedure where the protonation states of residues and molecules are allowed to fluctuate. This process is important in DNA binding, allostery, fibril formation, and other biological mechanisms. Simulating this using classical molecular dynamics can be surprisingly difficult. In this video, OpenMM Visiting Scholar Jerome Nilmeier describes his method to implement proton movements within the OpenMM molecular dynamics simulation software package.