Molecular Modeling

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Welcome to the Molecular Modeling community.

This community covers the full range of molecular modeling applications on GPUs. I invite group members to post links to recent publications, links to calls for participation for journals and conferences, and exchange example codes and ideas for GPU algorithms. I would especially like to maintain a bibliography of research papers on the use of GPUs in the many branches of molecular modeling, and would encourage others to contribute to the list of GPU papers that I've already started here.

John E. Stone, University of Illinois at Urbana-Champaign

Julie Mitchell, University of Wisconsin-Madison

Featured Stories and Papers

GPU Accelerated Molecular Docking with Parallel Genetic Algorithm (IEEE)

Abstract:

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GPU-Enabled Macromolecular Simulation: Challenges and Opportunities (IEEE)

Abstract:

GPU-enabled simulation of fully atomistic macromolecular systems is rapidly gaining momentum, enabled by massive parallelism and the parallelizability of various components of the underlying algorithms and methodologies. Here, we consider key aspects required for obtaining realistic macromolecular systems specifically adapted to GPUs; these aspects include realistic mathematical models and valid simulations.

Paper available at IEEE.

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GPU Enabled Macromolecular Simulation: Challenges and Opportunities (IEEE)

Abstract:

GPU enabled simulation of fully atomistic macromolecular systems is rapidly gaining momentum, enabled by the massive parallelism and due to parallelizability of various components of the underlying algorithms and methodologies. The massive parallelism in the order of several hundreds to few thousands of cores, presents opportunities as well poses implementation challenges. In this article we visit various key aspects of realism of macro molecular systems (i.e., the realism of mathematical models and the validity of simulations) specifically adapted to GPUs. We also visit some of the underlying challenges and solutions devised to tackle them.

Paper available at IEEE.

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