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A unified treatment for the fast and spectrally accurate evaluation of electrostatic potentials with periodic boundary conditions in any or none of the three spatial dimensions is presented. Ewald decomposition is used to split the problem into real-space and Fourier-space parts, and the Fast Fourier Transform (FFT)-based Spectral Ewald (SE) method is used to accelerate computation of the latter, yielding the total runtime O (N ⁡ log (N)) for N sources. A key component is a new FFT-based solution technique for the free-space Poisson problem. The computational cost is further reduced by a new adaptive FFT for the doubly and singly periodic cases, allowing for different local upsampling factors. The SE method is most efficient in the triply periodic case where the cost of computing FFTs is the lowest, whereas the rest of the algorithm is essentially independent of periodicity. We show that removing periodic boundary conditions from one or two directions out of three will only moderately increase the total runtime, and in the free-space case, the runtime is around four times that of the triply periodic case. The Gaussian window function previously used in the SE method is compared with a new piecewise polynomial approximation of the Kaiser–Bessel window, which further reduces the runtime. We present error estimates and a parameter selection scheme for all parameters of the method, including a new estimate for the shape parameter of the Kaiser–Bessel window. Finally, we consider methods for force computation and compare the runtime of the SE method with that of the fast multipole method. [ABSTRACT FROM AUTHOR]

The parallel scaling of classical molecular dynamics simulations is limited by the communication of the 3D fast Fourier transform of the particle-mesh electrostatics methods, which are used by most molecular simulation packages. The Fast Multipole Method (FMM) has much lower communication requirements and would, therefore, be a promising alternative to mesh based approaches. However, the abrupt switch from direct particle-particle interactions to approximate multipole interactions causes a violation of energy conservation, which is required in molecular dynamics. To counteract this effect, higher accuracy must be requested from the FMM, leading to a substantially increased computational cost. Here, we present a regularization of the FMM that provides analytical energy conservation. This allows the use of a precision comparable to that used with particle-mesh methods, which significantly increases the efficiency. With an application to a 2D system of dipolar molecules representative of water, we show that the regularization not only provides energy conservation but also significantly improves the accuracy. The latter is possible due to the local charge neutrality in molecular systems. Additionally, we show that the regularization reduces the multipole coefficients for a 3D water model even more than in our 2D example. [ABSTRACT FROM AUTHOR]