Related papers: Molecular Dynamics Simulations of Active Matter us…
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…
Only a small fraction of the data generated in state-of-the-art all-atom multi-microsecond molecular dynamics (MD) simulations is typically analyzed. With femtosecond integration steps, microsecond simulations generate billions of time…
In order to understand the physics phenomea on the fundamental aspects, the software simulations are a good exercise to succed in this way. Some work of heat transport and molecular physics laboratory are studied in a comparative mode…
Dynamic Movement Primitives (DMPs) is a framework for learning a point-to-point trajectory from a demonstration. Despite being widely used, DMPs still present some shortcomings that may limit their usage in real robotic applications.…
As the most important solvent, water has been at the center of interest since the advent of computer simulations. While early molecular dynamics and Monte Carlo simulations had to make use of simple model potentials to describe the atomic…
Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…
RUMD is a general purpose, high-performance molecular dynamics (MD) simulation package running on graphical processing units (GPU's). RUMD addresses the challenge of utilizing the many-core nature of modern GPU hardware when simulating…
The ability to perform ab initio molecular dynamics simulations using potential energies calculated on quantum computers would allow virtually exact dynamics for chemical and biochemical systems, with substantial impacts on the fields of…
The equations of classical mechanics can be used to model the time evolution of countless physical systems, from the astrophysical to the atomic scale. Accurate numerical integration requires small time steps, which limits the computational…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
The RMPCDMD software package performs hybrid Molecular Dynamics simulations, coupling Multiparticle Collision Dynamics to model the solvent and Molecular Dynamics to model suspended colloids, including hydrodynamics, thermal fluctuations,…
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…
Machine learning potentials (MLPs) have advanced rapidly and show great promise to transform molecular dynamics (MD) simulations. However, most existing software tools are tied to specific MLP architectures, lack integration with standard…
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD…
Quantum computing is gaining increased attention as a potential way to speed up simulations of physical systems, and it is also of interest to apply it to simulations of classical plasmas. However, quantum information science is…
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…
This paper has two main parts. The first one presents a direct path from microscopic dynamics to Debye screening, Landau damping and collisional transport. It shows there is more simplicity in microscopic plasma physics than previously…
A new methodology is developed to integrate numerically the equations of motion for classical many-body systems in molecular dynamics simulations. Its distinguishable feature is the possibility to preserve, independently on the size of the…
Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for a machine learning revolution and have already been profoundly impacted by the…
Open material databases storing hundreds of thousands of material structures and their corresponding properties have become the cornerstone of modern computational materials science. Yet, the raw outputs of the simulations, such as the…