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Normal mode partitioning of Langevin dynamics for biomolecules

By Christopher R. Sweet, Paula Petrone, Vijay S. Pande and Jesús A. Izaguirre

Abstract

We propose a novel normal mode multiple time stepping Langevin dynamics integrator called NML. 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. Our basis set uses the eigenvectors of a mass reweighted Hessian matrix calculated with a biomolecular force field. This particular choice has the advantage of an ordering according to the eigenvalues, which have a physical meaning of being the square 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. In NML, the higher frequency modes are overdamped and relaxed near their energy minimum while respecting the subspace of low frequency dynamical modes. Our 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, NML gives a twofold improvement in efficiency over plain Langevin dynamics 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) model, with good scaling with system size subject to the number of modes propagated. NML has been implemented in the open source software PROTOMOL

Topics: Biological Molecules, Biopolymers, and Biological Systems
Publisher: American Institute of Physics
OAI identifier: oai:pubmedcentral.nih.gov:2673189
Provided by: PubMed Central
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