PRAC - Hierarchical molecular dynamics sampling for assessing pathways and free energies of RNA catalysis, ligand binding, and conformational change

University Of Utah, Salt Lake City UT

Investigators

Abstract

This award facilitates scientific research using the large, new, computational resource named Blue Waters being developed by IBM and scheduled to be deployed at the University of Illinois in 2011. It provides travel funds to support technical coordination between the principal investigators, the Blue Waters project team and the vendor technical team. An experienced team of AMBER biomolecular simulation software developers with expertise ranging from QM/MM methods, enhanced sampling methods, code optimization and parallelization, and biomolecular simulation aim to enhance the AMBER software for optimal function on the Blue Waters machine. The intended application area involves RNA and the main goals are to hierarchically and tightly couple a series of optimized molecular dynamics engines to better map out the conformational, energetic and chemical landscape of RNA. The simulation engines will be optimized at the supernode level and will be coupled together and exchange information to better sample and interpret the free energy landscape. Broader impact and significance centers on ultimately providing a better understanding of RNA and protein structure, dynamics and function and the development, exploration, and integration of biomolecular simulation technologies to better understand and explore the structural, chemical and energetic landscapes of biomolecules. The latter impacts will translate to other application areas and emerging computer hardware.