Related papers: RBMD: A molecular dynamics package enabling to sim…

Algorithmic formulations of GPU programs provide a high-level alternative to device-specific code by expressing computations as compositions of well-defined parallel primitives (e.g., map, sort, reduce), rather than through handcrafted GPU…

Molecular simulation technologies have afforded researchers a unique look into the nanoscale interactions driving physical processes. However, a limitation for molecular dynamics (MD) simulations is that they must be performed on…

Micro-macro models provide a powerful tool to study the relationship between microscale mechanisms and emergent macroscopic behavior. However, the detailed microscopic modeling may require tracking and evolving a high-dimensional…

GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…

Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…

Many-body dispersion (MBD) is a powerful framework to treat van der Waals (vdW) dispersion interactions in density-functional theory and related atomistic modeling methods. Several independent implementations of MBD with varying degree of…

We introduce JAX MD, a software package for performing differentiable physics simulations with a focus on molecular dynamics. JAX MD includes a number of physics simulation environments, as well as interaction potentials and neural networks…

Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…

This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization…

In molecular dynamics (MD), systems are molecules made up of atoms, and the aim is to determine their evolution over time. MD is based on a numerical resolution algorithm, whose role is to apply the forces generated by the various…

We introduce an algorithm based on Generalized Dual Method (GDM) to efficiently study the dynamics of a particle in quasiperiodic environments without the need to use periodic approximations or to save the information of the vertices that…

One of application that needs high performance computing resources is molecular d ynamic. There is some software available that perform molecular dynamic, one of these is a well known GROMACS. Our previous experiment simulating molecular…

The recent introduction of Unified Virtual Memory (UVM) in GPUs offers a new programming model that allows GPUs and CPUs to share the same virtual memory space, which shifts the complex memory management from programmers to GPU driver/…

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales,…

This master thesis introduces the idea of dynamic cutoffs in molecular dynamics simulations, based on the distance between particles and the interface, and presents a solution for detecting interfaces in real-time. Our dynamic cutoff method…

Understanding the complex behavior of molecular systems is fundamental to fields such as physics, materials science, and biology. Molecular dynamics (MD) simulations are crucial tools for studying atomic-level dynamics. This work focuses on…

In many real-world scenarios, the underlying random fluctuations are non-Gaussian, particularly in contexts where heavy-tailed data distributions arise. A typical example of such non-Gaussian phenomena calls for L\'evy noise, which…

Molecular dynamics (MD) simulations employing classical force fields constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. However, the predictive power of these simulations is only as…

In this work we present an efficient implementation of Canonical Monte Carlo simulation for Coulomb many body systems on graphics processing units (GPU). Our method takes advantage of the GPU Single Instruction, Multiple Data (SIMD)…

This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software…