Development of a lattice-sum method emulating nonperiodic boundary conditions for the treatment of electrostatic interactions in molecular simulations: a continuum-electrostatics study.
Artifacts induced by the application of periodic boundary conditions and lattice-sum methods in explicit-solvent simulations of (bio-)molecular systems are nowadays a major concern in the computer-simulation community. The present article reports a first step toward the design of a modified lattice-sum algorithm emulating nonperiodic boundary conditions, and therefore exempt of such periodicity-induced artifacts. This result is achieved here in the (more simple) context of continuum electrostatics. It is shown that an appropriate modification of the periodic Poisson equation and of its boundary conditions leads to a continuum-electrostatics scheme, which, although applied under periodic boundary conditions, exactly mimics the nonperiodic situation. The possible extension of this scheme to explicit-solvent simulations is outlined and its practical implementation will be described in more details in a forthcoming article.
Kastenholz
Mika A
MA
Laboratorium für Physikalische Chemie, ETH Zürich, CH-8093 Zürich, Switzerland.
Hünenberger
Philippe H
PH
D000465:Algorithms; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D016012:Poisson Distribution; D011487:Protein Conformation; D012997:Solvents; D055672:Static Electricity; D013816:Thermodynamics
D012997:Solvents