Related papers: MDcraft -- a modern molecular dynamics simulation …
Recent developments in many-body potential energy representation via deep learning have brought new hopes to addressing the accuracy-versus-efficiency dilemma in molecular simulations. Here we describe DeePMD-kit, a package written in…
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…
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…
Molecular dynamics is a powerful simulation tool to explore material properties. Most of the realistic material systems are too large to be simulated with first-principles molecular dynamics. Classical molecular dynamics has lower…
Molecular dynamics (MD) simulation is a powerful tool for studying biomolecular structural changes, molecular recognition, transmembrane transport, and functional mechanisms. However, its practical bottleneck lies not only in software…
Molecular dynamics (MD) is a powerful tool for exploring the behavior of atomistic systems, but its reliance on sequential numerical integration limits simulation efficiency. We present a novel neural network architecture, MDtrajNet, and a…
Molecular dynamics simulations are an important tool for describing the evolution of a chemical system with time. However, these simulations are inherently held back either by the prohibitive cost of accurate electronic structure theory…
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited…
Molecular dynamics (MD) simulations provide considerable benefits for the investigation and experimentation of systems at atomic level. Their usage is widespread into several research fields, but their system size and timescale are also…
Molecular dynamics (MD) is a powerful and popular tool for understanding the dynamical evolution of materials at the nano and mesoscopic scales. There are various flavors of MD ranging from the high fidelity albeit computationally expensive…
Unraveling the dynamical motions of biomolecules is essential for bridging their structure and function, yet it remains a major computational challenge. Molecular dynamics (MD) simulation provides a detailed depiction of biomolecular…
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,…
Molecular dynamics (MD) simulations are essential for understanding biomolecular systems but remain challenging to automate. Recent advances in large language models (LLM) have demonstrated success in automating complex scientific tasks…
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…
Molecular dynamics simulations provide a mechanistic description of molecules by relying on empirical potentials. The quality and transferability of such potentials can be improved leveraging data-driven models derived with machine learning…
Multiparticle collision dynamics (MPCD) is a flexible and robust mesoscale computational technique for simulating solvent-mediated hydrodynamic interactions in soft materials. Here, we provide a critical overview of the MPCD method and…
PLUMED is an open-source software package that is widely used for analyzing and enhancing molecular dynamics simulations that works in conjunction with most available molecular dynamics softwares. While the computational cost of PLUMED…
In a world made of atoms, the computer simulation of molecular systems, such as proteins in water, plays an enormous role in science. Software packages that perform these computations have been developed for decades. In molecular…
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…
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…