Algorithm optimization in molecular dynamics simulation

2021

We propose a fast neighbor-list method for the calculation of short-range interactions in molecular dynamics simulations, typically the Lennard-Jones interaction. The so-called randomized Verlet list method introduces two-level neighbor lists for each particle, which are with the core-shell structure, such that particles in core and shell regions can be treated separately. Direct interactions are performed in the core region. For the shell zone, we employ a random batch of interacting particles to reduce the number of interaction pairs. We investigate the Lennard-Jones fluid by molecular dynamics simulations, demonstrate the error estimate, and show that this novel method can significantly accelerate the simulations with a factor of several fold without loss of the accuracy. This method is simple to implement and can be straightforwardly extended to other interactions such as Ewald short-range part, and is promising for large-scale molecular dynamics simulations.

Computer Physics Communications, 2004

An improved neighbor list algorithm is proposed to reduce unnecessary interatomic distance calculations in molecular simulations. It combines the advantages of Verlet table and cell linked list algorithms by using cell decomposition approach to accelerate the neighbor list construction speed, and data sorting method to lower the CPU data cache miss rate, as well as partial updating method to minimize the unnecessary reconstruction of the neighbor list. Both serial and parallel performance of molecular dynamics simulation are evaluated using the proposed algorithm and compared with those using conventional Verlet table and cell linked list algorithms. Results show that the new algorithm outperforms the conventional algorithms by a factor of 2 ∼ 3 in cases of both small and large number of atoms.

The Journal of Chemical Physics, 2021

We propose a fast method for the calculation of short-range interactions in molecular dynamics simulations. The so-called random-batch list method is a stochastic version of the classical neighbor-list method to avoid the construction of a full Verlet list, which introduces two-level neighbor lists for each particle such that the neighboring particles are located in core and shell regions, respectively. Direct interactions are performed in the core region. For the shell zone, we employ a random batch of interacting particles to reduce the number of interaction pairs. The error estimate of the algorithm is provided. We investigate the Lennard-Jones fluid by molecular dynamics simulations and show that this novel method can significantly accelerate the simulations with a factor of several fold without loss of the accuracy. This method is simple to implement, can be well combined with any linked cell methods to further speed up and scale up the simulation systems, and can be straightfo...

In this chapter a summary is given of the key ingredients necessary to carry out a molecular dynamics simulation, with particular emphasis on macromolecular systems. We discuss the form of the intermolecular potential for molecules composed of atoms, and of non-spherical sub-units, giving examples of how to compute the forces and torques. We also describe some of the MD algorithms in current use. Finally, we briefly refer to the factors that influence the size of systems, and length of runs, that are needed to calculate statistical properties.

2006

Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A perspective on the field of parallel md simulations is given. Hardware and software aspects are characterized and the interplay between the two is briefly discussed. A method for performing ab initio md is described; the method essentially recomputes the interaction potential at each time-step. It has been tested on a system of liquid water by comparing results with other simulation methods and experimental results. Different strategies for parallelization are explored. Furthermore, data-parallel methods for short-range and long-range interactions on massively parallel platforms are described and compared. Next, a method for treating electrostatic interactions in md simulations is developed. It combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform-ENUF for short. The method scales as O(N log N), where N is the number of charges in the system. ENUF has a behavior very similar to Ewald summation and can be easily and efficiently implemented in existing simulation programs. Finally, an outlook is given and some directions for further developments are suggested.

In this chapter a summary is given of the key ingredients necessary to carry out a molecular dynamics simulation, with particular emphasis on macromolecular systems. We discuss the form of the intermolecular potential for molecules composed of atoms, and of non-spherical sub-units, giving examples of how to compute the forces and torques. We also describe some of the MD algorithms in current use. Finally, we briefly refer to the factors that influence the size of systems, and length of runs, that are needed to calculate statistical properties.

Mathematical and Computer Modelling, 2005

This paper describes the performance of a portable molecular dynamics code running on an eight-node PC cluster. The molecular dynamics code is based on the atom decomposition method for distributing the computation load among the processors and the MPI protocol for managing communications among processors. We discuss the changes made to the serial code with an effort to maintain its readability. We examined the program performance for system sizes of order 102 to 104 atoms and number of processors varying from 1 to 8, by measuring the total execution time and the corresponding speedup, as well as the communication time for data exchange and the time for the calculation of interatomic forces. Using simple comnmnication and computation load considerations, we propose models in order to explain the observed behaviour and predict the optimal usage of the cluster. It turns out that using few parameters that can be easily measured one can predict quite accurately the optimal usage of small clusters running short range molecular dynamics programs.

Journal of Parallel and Distributed Computing, 2019

We present projection sorting, an algorithmic approach to determining pairwise short-range forces between particles in molecular dynamics simulations. We show it can be more effective than the standard approaches when particle density is non-uniform. We implement tuned versions of the algorithm in the context of a biophysical simulation of chromosome condensation, for the modern Intel Broadwell and Knights Landing architectures, across multiple nodes. We demonstrate up to 5× overall speedup and good scaling to large problem sizes and processor counts.

2010

The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new

2012 IEEE 8th International Conference on Intelligent Computer Communication and Processing, 2012

This paper concerns mainly with parallel and distributed implementations of molecular dynamics simulations of the Lennard-Jones potential model. The reported research work studies and experiments different algorithms and parallelization techniques for shared memory and message passing architectures, and the programs are executed on single-core processors, multicore processors, GPU, and GPU cluster. The solution based on efficient versions of the neighbor list algorithm and space division technique is further discussed. The obtained speedups for multicore processor, GPU, and GPU cluster, relative to the single-core processor implementation of the program, are analyzed, and the advantages of the algorithms are highlighted.