Normal Mode Partitioning of Langevin Dynamics for the Simulation of Biomolecules

Thursday, July 26, 2007 - 2:00pm - 2:40pm
EE/CS 3-180
Jesus Izaguirre (University of Notre Dame)
A novel Normal-Mode-Partitioned Langevin dynamics integrator is
proposed. The aim is to approximate the kinetics or
thermodynamics of a biomolecule by a reduced model based on a
normal mode decomposition of the dynamical space. The basis set
uses the eigenvectors of a mass re-weighted Hessian matrix
calculated with a biomolecular force field. This particular
choice has the advantage of an ordering according to the
eigenvalues, which has a physical meaning (square-root of the
mode frequency). Low frequency eigenvalues correspond to more
collective motions, whereas the highest frequency eigenvalues
are the limiting factor for the stability of the integrator.
The higher frequency modes are overdamped and relaxed near to
their energy minimum while respecting the subspace of low
frequency dynamical modes. Numerical results confirm that both
sampling and rates are conserved for an implicitly solvated
alanine dipeptide model, with only 30% of the
modes propagated, when compared to the full model. For
implicitly solvated systems the method can be shown to give
improvements in efficiency more than 2 times even for sampling
a small 22 atom (alanine dipeptide) model and in excess of an
order of magnitude for sampling an 882 atom (bovine pancreatic
trypsin inhibitor, or BPTI) model, with good scaling with
system size subject to the number of modes propagated.