Paper Citing NAMD - Abstract
Karttunen, Mikko; Rottler, Joerg; Vattulainen, Ilpo; Sagui, Celeste
Electrostatics in biomolecular simulations: Where are we now and where are we heading?
COMPUTATIONAL MODELING OF MEMBRANE BILAYERS, 60:49-89, 2008
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.
