Molecular Dynamics Simulation

Profacgen studies molecular dynamics of protein systems using state-of-the-art software tools. The general workflow of our MD simulation service follows these steps: First, a model system is selected, in which missing segments are fixed and the protonation states determined. Then the system is energy minimized and equilibrated by solving Newton's equations of motion until the properties of the system no longer change with time. After equilibration, a production run is performed for an appropriate period of time to output trajectories, which are then analyzed for the properties of interest.