Related papers: Accelerating Molecular Dynamics Simulations using …
We present an NPT extension of Ewald summation with prolates (ESP), a spectrally accurate and scalable particle-mesh method for molecular dynamics simulations of periodic, charged systems. Building on the recently introduced ESP framework,…
Fast Ewald summation efficiently evaluates Coulomb interactions and is widely used in molecular dynamics simulations. It is based on a split into a short-range and a long-range part, where evaluation of the latter is accelerated using the…
The smooth particle mesh Ewald (SPME) method is the standard method for computing the electrostatic interactions in the molecular simulations. In this work, the multiple staggered mesh Ewald (MSME) method is proposed to boost the accuracy…
The smooth particle mesh Ewald (SPME) method is an FFT based method for the fast evaluation of electrostatic interactions under periodic boundary conditions. A highly optimized implementation of this method is available in GROMACS, a widely…
Standard Ewald sums, which calculate e.g. the electrostatic energy or the force in periodically closed systems of charged particles, can be efficiently speeded up by the use of the Fast Fourier Transformation (FFT). In this article we…
Molecular Dynamics (MD) simulations play a central role in physics-driven drug discovery. MD applications often use the Particle Mesh Ewald (PME) algorithm to accelerate electrostatic force computations, but efficient parallelization has…
Computer simulations of model systems are widely used to explore striking phenomena in promising applications spanning from physics, chemistry, biology, to materials science and engineering. The long range electrostatic interactions between…
Coulomb interaction, following an inverse-square force-law, quantifies the amount of force between two stationary and electrically charged particles. The long-range nature of Coulomb interactions poses a major challenge to molecular…
For inhomogeneous systems with interfaces, the inclusion of long-range dispersion interactions is necessary to achieve consistency between molecular simulation calculations and experimental results. For accurate and efficient incorporation…
To evaluate electrostatics interactions, Molecular dynamics (MD) simulations rely on Particle Mesh Ewald (PME), an O(Nlog(N)) algorithm that uses Fast Fourier Transforms (FFTs) or, alternatively, on O(N) Fast Multipole Methods (FMM)…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
We develop a random batch Ewald (RBE) method for molecular dynamics simulations of particle systems with long-range Coulomb interactions, which achieves an $O(N)$ complexity in each step of simulating the $N$-body systems. The RBE method is…
Ewald summation is an important technique used to deal with long-range Coulomb interaction. While it is widely used in simulations of molecules and solid state materials, many important results are dispersed in literature and their…
We have extended the multilevel summation (MLS) method, originally developed to evaluate long-range Coulombic interactions in molecular dynamics (MD) simulations [Skeel et al., J. Comput. Chem., 23, 673 (2002)], to handle dispersion…
We evaluate the practical performance of the zero-multiple summation method (ZMM), a method for approximately calculating electrostatic interactions in molecular dynamics simulations. The performance of the ZMM is compared with that of the…
A crucial aspect in the simulation of electrochemical interfaces consists in treating the distribution of electronic charge of electrode materials that are put in contact with an electrolyte solution. Recently, it has been shown how a…
Quasi-2D Coulomb systems are of fundamental importance and have attracted much attention in many areas nowadays. Their reduced symmetry gives rise to interesting collective behaviors, but also brings great challenges for particle-based…
In computational molecular science, calculation of electrostatic interactions involving charged atoms - the strongest interactions in condensed phases, is a major bottleneck. We propose a quantum-classical algorithm for fast, yet, accurate…
The three most common methods, Ewald, fast multipole (FMM) and the particle-particle particle-mesh (PPPM), used to compute the interactions in many body Coulombic systems are compared for single and multi-processor machines. The Ewald…
The ENUF method, i.e., Ewald summation based on the Non-Uniform FFT technique (NFFT), is implemented in Dissipative Particle Dynamics (DPD) simulation scheme to fast and accurately calculate the electrostatic interactions at mesoscopic…