Biomolecular Simulation Using Amber and CHARMM

Case, David A. ; Brooks, Charles L., III

The Scripps Research Institute

关键词: Amber;    Computers;    Implementation;    59 Basic Biological Sciences;    Proteins;   

DOI  :  10.2172/835140
RP-ID  :  NONE
RP-ID  :  FG03-01ER25496
RP-ID  :  835140

美国|英语

来源: UNT Digital Library

【 摘 要 】

This project supports the development of software using terascale computers to carry out molecular simulations of protein function and macromolecular interactions. We are building on the existing CHARMM and Amber simulation packages, adapting them in novel ways to massively parallel architectures and high-performance CPUs. Three principal avenues being pursued are: (1) Improvements in load-balancing and communication for large-scale particle-mesh Ewald (PME) simulations of solvated biomolecules. (2) Modern techniques for accelerating convergence of sampling of configuration space offer promise for further exploitation of massively parallel architectures. These methods include parallel tempering and ''lambda dynamics'' procedures that connect multiple, synchronized results from PME simulations like those described in part [1]. (3) The implementation of efficient and scalable algorithms that move towards lower-resolution models in ways that can be carefully calibrated against atomic-level solvated simulations.