Simbios Talk by Jesus Izaguirre, Stanford University, June 6, 2007

Title: Normal mode splitting of Langevin dynamics applied to biomolecules

We propose a novel integrator for Langevin dynamics of biomolecules, which is capable of very long time steps. It is based on a splitting of the system using normal modes. Low frequency modes are propagated at the temperature of interest, whereas high frequency modes are relaxed using force minimization. Simulations show that with 10%-30% of the modes in small peptides and proteins one can recover kinetics and sampling. Speedups of over an order of magnitude are achieved for the bovine pancreatic trypsin inhibitor (BPTI). This is a collaboration with Chris Sweet (Notre Dame) and Paula Petrone and Vijay Pande (Stanford University).