相关论文: Particle Mesh Ewald for Molecular Dynamics in Open…

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.…

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)…

The evaluation of long-range Coulomb interactions is a significant cost in molecular dynamics (MD), even when using Particle Mesh Ewald (PME) or Particle-Particle-Particle-Mesh (PPPM) methods, which rely on Ewald splitting and the fast…

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…

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…

The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but…

Classical molecular dynamics (MD) simulations are important tools in life and material sciences since they allow studying chemical and biological processes in detail. However, the inherent scalability problem of particle-particle…

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…

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…

This paper introduces a random-batch molecular dynamics (RBMD) package for fast simulations of particle systems at the nano/micro scale. Different from existing packages, the RBMD uses random batch methods for nonbonded interactions of…

Due to its flexible architecture, FPGAs support unique, deep hardware pipeline implementations for accelerating HPC applications. However, these devices are quite new in the HPC space, and thus, have been scarcely explored outside some…

Molecular dynamics (MD) simulation is one of the past decade's most important tools for enabling biology scientists and researchers to explore human health and diseases. However, due to the computation complexity of the MD algorithm, it…

Scalable and efficient numerical simulations continue to gain importance, as computation is firmly established as the third pillar of discovery, alongside theory and experiment. Meanwhile, the performance of computing hardware grows through…

Particle Mesh Ewald (PME) methods accelerated through Fast Fourier Transforms (FFTs) for their reciprocal part are widely used to solve N -body problems over periodic structures with Laplace-like kernels. The FFT dependence of classical PME…

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…

The random batch Ewald (RBE) is an efficient and accurate method for molecular dynamics (MD) simulations of physical systems at the nano-/micro- scale. The method shows great potential to solve the computational bottleneck of long-range…

Molecular Dynamics (MD) codes predict the fundamental properties of matter by following the trajectories of a collection of interacting model particles. To exploit diverse modern manycore hardware, efficient codes must use all available…

Although poor for small dynamic scales, the Particle-Mesh (PM) model allows in astrophysics good insight for large dynamic scales at low computational cost. Furthermore, it is possible to employ a very high number of particles to get high…

We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…

Field-Programmable Gate Arrays (FPGAs) are widely used in the central signal processing design of the Square Kilometre Array (SKA) as acceleration hardware. The frequency domain acceleration search (FDAS) module is an important part of the…