Biomolecular Simulation Using Amber and CHARMM

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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 ... continued below

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Case, David A. & Brooks, Charles L., III November 29, 2004.

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Description

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.

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  • Report No.: NONE
  • Grant Number: FG03-01ER25496
  • DOI: 10.2172/835140 | External Link
  • Office of Scientific & Technical Information Report Number: 835140
  • Archival Resource Key: ark:/67531/metadc780632

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

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  • November 29, 2004

Added to The UNT Digital Library

  • Dec. 3, 2015, 9:30 a.m.

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  • June 17, 2016, 3:04 p.m.

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Case, David A. & Brooks, Charles L., III. Biomolecular Simulation Using Amber and CHARMM, report, November 29, 2004; United States. (digital.library.unt.edu/ark:/67531/metadc780632/: accessed July 16, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.