Ewald sums

When carried out properly, the results of the reaction field method and the Ewald sum are consistent [67]. Recently, the reaction field method has been reconnnended on grounds of elTiciency and ease of progrannning [68, 69]. The... 

Gray C G, Sainger Y S, Joslin C G, Cummings P T and Goldman S 1986 Computer simulation of dipolar fluids. Dependence of the dielectric constant on system size a comparative study of Ewald sum and reaction field approaches J. Chem. Phys. 85 1502-4... 

Darden T, York D and Pedersen L 1993 Particle mesh Ewald—an N.log(N) method for Ewald sums in large systems J. Chem. Phys. 98 10089-92... 

Smith W 1992 A replicated data molecular dynamics strategy for the parallel Ewald sum Comput. Phys. Commun. 67 392-406... 

One of the most efficient algorithms known for evaluating the Ewald sum is the Particle-mesh Ewald (PME) method of Darden et al. [8, 9]. The use of Ewald s trick of splitting the Coulomb sum into real space and Fourier space parts yields two distinct computational problems. The relative amount of work performed in real space vs Fourier space can be adjusted within certain limits via a free parameter in the method, but one is still left with two distinct calculations. PME performs the real-space calculation in the conventional manner, evaluating the complementary error function within a cutoff... 

Desemo M and C Holm 1998a. How to Mesh Up Ewald Sums. I. A Theoretical and Numerical Comparison of Various Particle Mesh Routines. Journal of Chemical Physics 109 7678-7693. 

Regardless of which algorithm is used for fast calculation of Ewald sums, the computational cost is now competitive with the cost of cutoff calculations, and there is no longer a need to employ cutoffs for purposes of efficiency. Since Ewald summation is the natural expression of Coulomb s law in periodic boundary conditions, it is the recommended approach if periodic boundary conditions are to be used in a simulation. 

Eor instance, the contribution of water beyond 12 A from a singly charged ion is 13.7 kcal/mol to the solvation free energy or 27.3 kcal/mol to the solvation energy of that ion. The optimal treatment is to use Ewald sums, and the development of fast methods for biological systems is a valuable addition (see Chapter 4). However, proper account must be made for the finite size of the system in free energy calculations [48]. 

In order to And rjopt, we minimise an expression of the total CPU time, T, required for the Ewald sums. We assume that T is proportional to the number of vectors used in both the reciprocal and direct space sums, G /(2j ) and R /a . and to t, and t<, the CPU times required for the evaluation of a single term in each series. In formulae. 

In this section we describe the methods to extend Ewald sum methodologies to accelerate the calculation of the intermolecular interactions using PBC. For simplicity, we begin with a generalization of Ewald sums to interacting spherical Hermite Gaussians (e.g. GEM-0 [14]). This is followed by the extension to arbitrary angular momentum. Finally, we describe the implementation of methods to speed up both the direct an reciprocal terms in the Ewald sum [62],... 

There are problems with using both of these methods in the simulation of inhomogeneous systems. Because the periodicity of the system is lost in the direction normal to the interface (unless one uses image charges with the flat wall model, which effectively results in a 3D periodic system implementation of the ES method is not straightforward for certain type of systems. Hautman and Klein have presented a modified Ewald sum method for the simulation of systems that are periodic in two... 

An analogous implementation for the standard Ewald method has been presented [44]. Conversely, direct use of the Ewald sum [45] or approximations to it [46 18], which are pairwise decomposable and hence suitable for MC simulations, have generally proven to be too inefficient for most modern applications [49]. Additionally, it should be pointed out that Ewald sums — independent of implementation — are incompatible with implicit solvent models that model a spatially varying dielectric with anything more than trivial functional dependencies [45]. 

In infinite periodic systems, an attractive alternative to the use of a cut-off distance is the Ewald sum technique, first described for chemical systems by York, Darden and Pedersen (1993). By using a reciprocal-space technique to evaluate long-range contributions, the total electrostatic interaction can be calculated to a pre-selected level of accuracy (i.e., the Ewald sum limit is exact) witli a scaling that, in tlie most favorable case (called Particle-mesh Ewald , or PME), is AlogA. Prior to the introduction of Ewald sums, the modeling of polyelectrolytes (e.g., DNA) was rarely successful because of the instabilities introduced... 

As already noted in Chapter 2, for electrostatic interactions, Ewald sums are generally to be preferred over cut-offs because of tlie long-range nature of the interactions. For van der Waals type terms, cut-offs do not introduce significant artifacts provided they are reasonably large (typically 8-12 A). 

In infinite periodic systems, an attractive alternative to the use of a cut-off distance is the Ewald sum technique, first described for chemical systems by York, Darden and Pedersen (1993). By using a reciprocal-space technique to evaluate long-range contributions, the total... 

---