Ewald summation extended system

In recent years, a number of models have been introduced which permit the inclusion of long-range electrostatic interactions in molecular dynamics simulation. For simulations of proteins and enzymes in a crystalline state, the Ewald summation is considered to be the correct treatment for long range electrostatic interactions (Ewald 1921 Allen and Tildesley 1989). Variations of the Ewald method for periodic systems include the particle-mesh Ewald method (York et al. 1993). To treat non-periodic systems, such as an enzyme in solution other methods are required. Kuwajima et al. (Kuwajima and Warshel 1988) have presented a model which extends the Ewald method to non-periodic systems. Other methods for treating explicitly long-range interactions... 

Essential dynamics, 2, 233, 236, 242-244, 247 Euler angles, 3,168 evolutionary determinants, 4, 4, 5 evolvability, 4, 7-9,17 Ewald summation, 2, 265 Ewald summation techniques, 1, 59, 62, 75 exact exchange, 1, 26, 27 exchange repulsion, 3,179,180 excited state structure/dynamics, 1, 24 excretion see ADMET properties explicit-rl2 correlation, 5, 132,140 explicit solvent, 2, 98, 99,101,102,104-106 exponential damping functions, 3,180 extended systems, 1, 26... 

Hummer G, Grdnbech-Jensen N, Neumann M. Pressure calculation in polar and charged systems using Ewald summation results for the extended simple point charge model of water. J. Chem. Phys. 1998 109 2791. 

The Na-AOT reverse micelle is a widely investigated reverse micelle system made up of the sodium salt of a two-tailed anionic surfactant, sodium di(2-ethylhexyl) sulfosuccinate. The interior of the aqueous reverse micelle is modeled as a rigid cavity, with a united atom representation for the sulfonate head group (Faeder and Ladanyi 2000 Pal et al. 2005). The head groups protrude from the cavity boundary and are tethered only in the radial direction by means of a harmonic potential. Interactions between reverse micelles are neglected in the model hence periodic boundary conditions and Ewald summations for the electrostatics are not required. Water is treated using the extended simple point charge, or SPC/E, model and the potential parameters for all the species are listed in Table 6.1. 

Regardless of the type of model used, a method must be chosen for the self-consistent solution of the polarizable degrees of freedom. Direct solution via matrix inversion is nearly always avoided by most researchers in the field, because of the prohibitive O(N ) scaling with system size, N. Both iterative and predictive methods reduce the scaling to match that of the potential evaluation [O(N ) for direct summation 0(N In N) for Ewald-based meth-ods ° " 0 N) if interactions are neglected beyond some distance cutoff], but the cost of the iterations means that the predictive methods are always more efficient. Extended Lagrangian methods have been implemented for all four types of polarizable... 

---