CHARMM (Chemistry at Harvard Macromolecular Mechanics) has been a primary research tool for macromolecular simulations and modeling in biology for over two decades. During this period, CHARMM development, and applications emerging from its use, have defined the field of biomolecular computation. This proposal is aimed at ensuring CHARMM will continue as the development platform for future generations of scientists by addressing components of the software and its attendant support infrastructure that represent bottlenecks in development, performance and maintenance. Specifically, antiquated FORTRAN source will be transformed into a more modular structure exploiting programming paradigms and methods from FORTRAN 95/2003 and C. Memory management and data structures will be reorganized in a more object- oriented manner to improve the memory footprint while enabling large systems to be studied without timely reconfiguration and recompilation. This restructuring will be done in conjunction with improvements to underlying computational kernels in CHARMM, which will significantly enhance single processor performance and improve parallel scaling. Emphasis will be given to improving parallelism for two target system sizes. For systems of 50-200K atoms, which represent many typical applications, we will develop, adapt and deploy methods that yield good parallel efficiency (greater than 70%) for tightly coupled parallelism in molecular dynamics on department accessible parallel platforms (~100 commodity processors with a high bandwidth interconnect). For large biological problems on large supercomputers, i.e. for systems approaching 1M atoms running on 0.5-2K processors, we will develop and implement new simulation kernels for CHARMM that exploit the large spatial dimensions of these systems and employ techniques of spatial decomposition and task-level parallelism. To ensure future maintainability and usability, we will streamline the installation and testing protocols and overhaul the existing documentation. The outcome of these efforts will be a program platform that will facilitate continued forefront research in macromolecular simulation and modeling and enable its continued development and maintenance for future generations of researchers.
CHARMM (Chemistry at Harvard Macromolecular Mechanics) has been a primary research tool for macromolecular simulations and modeling in biology for over two decades, assisting biomedical researchers in theoretical investigations of protein-ligand interactions, enzyme mechanism, protein folding, free energy and docking simulations for drug discovery and design, and a large range of other applications in protein, nucleic acid and membrane modeling. The nearly 8000 citations to CHARMM support this pivotal role of this software package to the biomedical community.
The aims of this proposal are to modernize, improve performance, and secure a solid pathway for continued development of the CHARMM package to ensure its ongoing availability for biomedical researchers. ? ? ?
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| Petrella, Robert J (2011) A versatile method for systematic conformational searches: application to CheY. J Comput Chem 32:2369-85 |
| Brooks, B R; Brooks 3rd, C L; Mackerell Jr, A D et al. (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30:1545-614 |
