Example Simulation

Video of Hybrid MD/MC: Inserting Water in BPTI’s Binding Pocket

Utilizing the hybrid molecular dynamics (MD)/Monte Carlo (MC) simulation, water is inserted into the buried binding pocket of the bovine pancreatic trypsin inhibitor (BPTI). The hybrid NAMD/GOMC simulation produces water in the binding pocket orders of magnitude faster than when using MD alone. The hybrid simulation is capable of producing faster and more accurate results because the MC moves allow waters to be quickly inserted and do not solely rely on diffusion of water into the BPTI binding pocket.

The green protein and waters (spheres) represent the crystallography data. The purple protein and red/white water are the simulated system.