Concepedia

Biomolecular electrostatics using a fast multipole BEM on up to 512 gpus and a billion unknowns

Rio Yokota, Jaydeep P. Bardhan, Matthew G. Knepley, Lorena A. Barba, Tsuyoshi Hamada

Computer Physics Communications · 2011 · 84 citations · 94 references

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Concepts

References

94

VMD: Visual molecular dynamics

William Humphrey, Andrew Dalke, Klaus Schulten · Journal of Molecular Graphics · 1996 · 66.6K citations

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The Protein Data Bank

Helen M. Berman · Nucleic Acids Research · 2000 · 39.8K citations

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Particle mesh Ewald: An <i>N</i>⋅log(<i>N</i>) method for Ewald sums in large systems

Tom Darden, Darrin M. York, Lee G. Pedersen · The Journal of Chemical Physics · 1993 · 30.7K citations · Full text

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Scalable molecular dynamics with NAMD

J. C. Phillips, Rosemary Braun, Wei Wang et al. · Journal of Computational Chemistry · 2005 · 17.4K citations · Full text

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<scp>CHARMM</scp>: A program for macromolecular energy, minimization, and dynamics calculations

Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson et al. · Journal of Computational Chemistry · 1983 · 14.9K citations

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