Chapter 2 Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading?

Publication Type
Book Chapter
Year of Publication
2008
Authors
Karttunen, Mikko
Rottler, Jörg
Vattulainen, Ilpo
Sagui, Celeste
Scott E. Feller
Name of Publication
Computational Modeling of Membrane Bilayers
Volume
Volume 60
Pagination
49–89
Publisher
Academic Press
ISBN Number
1063-5823
Abstract

In this review, we discuss current methods and developments in the treatment of electrostatic interactions in biomolecular and soft matter simulations. We review the current ‘work horses’, namely, Ewald summation based methods such the {Particle-Mesh} Ewald, and others, and also newer real-space methods such as multigrid methods, and local algorithms for Coulomb's law. We also pay attention to boundary conditions. Although periodic boundary conditions are used most commonly, it is often desirable to have systems that are confined or have boundaries. Finally, we briefly describe some current and available software for the computation of electrostatics in biomolecular and soft matter simulations.


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