The u-series: A separable decomposition for electrostatics computation with improved accuracy.

@article{Predescu2019TheUA,
  title={The u-series: A separable decomposition for electrostatics computation with improved accuracy.},
  author={Cristian Predescu and Adam K. Lerer and Ross Lippert and Brian Towles and Jerry P. Grossman and Robert M. Dirks and David E. Shaw},
  journal={The Journal of chemical physics},
  year={2019},
  volume={152 8},
  pages={
          084113
        }
}
The evaluation of electrostatic energy for a set of point charges in a periodic lattice is a computationally expensive part of molecular dynamics simulations (and other applications) because of the long-range nature of the Coulomb interaction. A standard approach is to decompose the Coulomb potential into a near part, typically evaluated by direct summation up to a cutoff radius, and a far part, typically evaluated in Fourier space. In practice, all decomposition approaches involve… 

Midtown splines: An optimal charge assignment for electrostatics calculations.

Midtown splines are described that achieve fourth- and sixth-order accuracy in the grid spacing while requiring a support size of 32 and 88 grid nodes, respectively, compared to the 64 and 216 nodes required by the most widely used transfer functions (B-splines).

Multilevel summation for periodic electrostatics using B-splines.

A realization of the MSM, which can be regarded as a multilevel extension of the (smoothed) particle mesh Ewald (PME) method, but with the Ewald softening replaced by one having a finite range.

Random batch sum-of-Gaussians method for molecular dynamics simulations of particle systems

An accurate, highly efficient and scalable random batch sum-of-Gaussians (RBSOG) method for molecular dynamics simulations of systems with long-range interactions, promising to construct fast algorithms of a series of molecular dynamics methods for various interacting kernels.

Improved Random Batch Ewald Method in Molecular Dynamics Simulations.

An improved RBE method for the nonbonding interactions is presented by introducing the random batch idea to constructing neighbor lists for the treatment of both the short-range part of the Ewald splitting and the Lennard-Jones potential.

Hardware Acceleration of Tensor-Structured Multilevel Ewald Summation Method on MDGRAPE-4A, a Special-Purpose Computer System for Molecular Dynamics Simulations

A co-design of the MDGRAPE-4A and the novel algorithm, tensor-structured multilevel Ewald summation method (TME), which produced hardware modules on the custom LSI circuit for particle-grid operations and for grid-grid separable convolutions on a 3D torus network.

Accelerators for Classical Molecular Dynamics Simulations of Biomolecules

The goal is to summarize the fundamental algorithms that are employed in the literature to then highlight the challenges that have affected accelerator implementations in practice, and provide insights into the potential of emerging hardware platforms and algorithms for MD.

Anton 3: Twenty Microseconds of Molecular Dynamics Simulation Before Lunch

  • D. ShawP. Adams Kevin Yuh
  • Biology
    SC21: International Conference for High Performance Computing, Networking, Storage and Analysis
  • 2021
The main architectural and algorithmic developments that were necessary to achieve significant improvements in time-to-solution over its predecessor, Anton 2, and over 100-fold faster than any other currently available supercomputer are presented.

High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2

This work investigated the significance of six commonly observed spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations and used other binding free energy prediction methods and compared the results with the experimental data if available.

Autoregulation of a trimeric transporter involves the cytoplasmic domains of both adjacent subunits

Molecular simulations of the BetP trimer provide a molecular framework for the arrangement of the terminal domains in the downregulated protein and indicates an intricate interplay between the three protomers of BetP and, specifically, a multi-directionality that may facilitate autoregulation of betaine transport.

An OpenCL 3D FFT for Molecular Dynamics Simulations on Multiple FPGAs

This work presents a distributed OpenCL 3D FFT implementation on Intel Stratix 10 FPGAs for grids up to 128 Gbps, which outperforms GPUs for smaller FFTs, even without distribution.

References

SHOWING 1-10 OF 45 REFERENCES

An optimized method for treating long-range potentials

Abstract In simulations of systems with periodic boundary conditions, the Ewald image method is used to evaluate long-range potentials by constructing infinite but rapidly converging sums in both…

Isotropic periodic sum: a method for the calculation of long-range interactions.

This work presents an accurate and efficient approach to the calculation of long-range interactions for molecular modeling and simulation using the isotropic periodic sum method, which can be applied to potentials of any functional form and to fully and partially homogenous systems as well as finite systems.

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling.

A novel real space multigrid approach that handles Coulomb interactions very effectively and implement it in the CP2K code is presented, leading to a dynamics with very good energy conservation.

Simulation of electrostatic systems in periodic boundary conditions. I. Lattice sums and dielectric constants

The effective interactions of ions, dipoles and higher-order multipoles under periodic boundary conditions are calculated where the array of periodic replications forms an infinite sphere surrounded…

New splitting formulations for lattice summations

A new formulation for the efficient evaluation of pairwise interactions for large nonperiodic or spatially periodic infinite lattices is presented and it is shown that a polynomial multiplication to the Gaussian core function can be used to formulate desired mathematical or physical characteristics into a lattice summation method.

An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations.

Results from QM/MM calculations with periodic boundary conditions (PBC) show that the use of PBC is essential when studying highly ordered crystal structures, unless a carefully designed MM crystal is used for the calculation.

An algorithm for the simulation of condensed matter which grows as the 3/2 power of the number of particles

Current supercomputers and the impending availability of large scale parallel machines makes possible the study by molecular dynamics of a number of fundamental problems in condensed matter science…

Molecular dynamics simulations of biomolecules: long-range electrostatic effects.

The basic issues for an accurate representation of the relevant electrostatic interactions are introduced and the Ewald summation methods, the fast particle mesh methods, and the fast multipole methods are discussed.

Theory of the expansion of wave functions in a gaussian basis

The convergence properties of the expansions of the function 1/r and the function exp(-Ξ±r) in an even-tempered basis of Gaussians are studied analytically and the minimum overall error is reached.