Molecular Dynamics Computer simulations are used to compute trajectories of all atoms in a molecule, such as a protein. From such trajectories important information about the system is obtained that can be used for example to develop new drugs against diseases. However, because a main assumption in molecular dynamics is that chemical bonds are modelled as springs, and therefore bonds cannot break. This is problematic because in reality bonds involving protons break all the time. To include this important aspect of reality in the molecular dynamics simulations, we had previously developed a method that we will now use on modern supercomputers to address two important problems in structural biology: (i) How do biomolecules recognize or sense each other, and (ii) what is the mechanism by which proteins can convert chemical energy into mechanical work.

2026

2028