Related papers: RBMD: A molecular dynamics package enabling to sim…
DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials (MLP) known as Deep Potential (DP) models. This package, which was released in 2017, has been widely…
Discrete particle simulations have become the standard in science and industrial applications exploring the properties of particulate systems. Most of such simulations rely on the concept of interacting spherical particles to describe the…
Molecular Dynamics (MD) simulation is a powerful tool for understanding the dynamics and structure of matter. Since the resolution of MD is atomic-scale, achieving long time-scale simulations with femtosecond integration is very expensive.…
Cardiovascular disease affects millions of people worldwide and its social and economic cost clearly motivates scientific research. Computer simulation can lead to a better understanding of cardiac physiology, and for pathology presents…
Two-dimensional Raman and hybrid terahertz/Raman spectroscopic techniques provide invaluable insight into molecular structure and dynamics of condensed-phase systems. However, corroborating experimental results with theory is difficult due…
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…
Polymerization of C60 molecular crystal under high pressure and high temperature is simulated by using linear scaling tight binding molecular dynamics (TBMD) with Graphic Processing Unit (GPU) as a computational accelerator for…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
In this work, we develop a random batch sum-of-Gaussians (RBSOG) method for molecular dynamics simulations of charged systems in the isothermal-isobaric (NPT) ensemble. We introduce an SOG splitting of the pressure-related $1/r^3$ kernel,…
This paper discusses a numerical method for computing the evolution of large interacting system of quantum particles. The idea of the random batch method is to replace the total interaction of each particle with the $N-1$ other particles by…
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…
Path-integral molecular dynamics (PIMD) simulations are crucial for accurately capturing nuclear quantum effects in materials. However, their computational intensity and reliance on multiple software packages often limit their applicability…
We introduce a scheme for molecular simulations, the Deep Potential Molecular Dynamics (DeePMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data.…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
This article presents new algorithms for massively parallel granular dynamics simulations on distributed memory architectures using a domain partitioning approach. Collisions are modelled with hard contacts in order to hide their…
The ring polymer molecular dynamics (RPMD) rate theory is an efficient and accurate method for estimating rate coefficients of chemical reactions affected by nuclear quantum effects. The commonly used RPMD treatment of gas-phase bimolecular…
This paper presents the RBG-Maxwell framework, a relativistic collisional plasma simulator on GPUs. We provide detailed discussions on the fundamental equations, numerical algorithms, implementation specifics, and key testing outcomes. The…
The accurate simulation of complex biochemical phenomena has historically been hampered by the computational requirements of high-fidelity molecular-modeling techniques. Quantum mechanical methods, such as ab initio wave-function (WF)…