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Molecular dynamics (MD) simulation predicts the trajectory of atoms by solving Newton's equation of motion with a numeric integrator. Due to physical constraints, the time step of the integrator need to be small to maintain sufficient…

计算物理 · 物理学 2021-12-22 Tianze Zheng , Weihao Gao , Chong Wang

Quantum mechanics based ab-initio molecular dynamics (MD) simulation schemes offer an accurate and direct means to monitor the time-evolution of materials. Nevertheless, the expensive and repetitive energy and force computations required in…

材料科学 · 物理学 2014-10-14 Venkatesh Botu , Rampi Ramprasad

Accurate prediction of energy and forces for 3D molecular systems is one of fundamental challenges at the core of AI for Science applications. Many powerful and data-efficient neural networks predict molecular energies and forces from…

化学物理 · 物理学 2026-04-23 Ali Mollahosseini , Mohammed Haroon Dupty , Wee Sun Lee

Molecular dynamics (MD) simulation is essential for various scientific domains but computationally expensive. Learning-based force fields have made significant progress in accelerating ab-initio MD simulation but are not fast enough for…

机器学习 · 计算机科学 2023-08-29 Xiang Fu , Tian Xie , Nathan J. Rebello , Bradley D. Olsen , Tommi Jaakkola

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…

计算物理 · 物理学 2021-01-11 Zun Wang , Chong Wang , Sibo Zhao , Shiqiao Du , Yong Xu , Bing-Lin Gu , Wenhui Duan

Exascale computing holds great opportunities for molecular dynamics (MD) simulations. However, to take full advantage of the new possibilities, we must learn how to focus computational power on the discovery of complex molecular mechanisms,…

化学物理 · 物理学 2019-01-16 Hendrik Jung , Roberto Covino , Gerhard Hummer

The core of molecular dynamics simulation fundamentally lies in the interatomic potential. Traditional empirical potentials lack accuracy, while first-principles methods are computationally prohibitive. Machine learning interatomic…

机器学习 · 计算机科学 2026-03-25 Shuyu Bi , Zhede Zhao , Qiangchao Sun , Tao Hu , Xionggang Lu , Hongwei Cheng

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…

定量方法 · 定量生物学 2026-04-22 Zhenyu Ma , Chunyi Yang , Yuyang Song , Jingyi Zhu , Letian Yang , Limei Xu , Min Xiao , Xukai Jiang

Despite its widespread use in materials science, conventional molecular dynamics (MD) simulations are severely constrained by timescale limitations. To address this shortcoming, we propose an empirical formulation of accelerated MD method,…

材料科学 · 物理学 2025-12-10 Liang Wan , Qingsong Mei , Haowen Liu , Huafeng Zhang , Jun-Ping Du , Shigenobu Ogata , Wen Tong Geng

While machine learning (ML) models have been able to achieve unprecedented accuracies across various prediction tasks in quantum chemistry, it is now apparent that accuracy on a test set alone is not a guarantee for robust chemical modeling…

Molecular dynamics (MD) simulations underpin modern computational drug discovery, materials science, and biochemistry. Recent machine learning models provide high-fidelity MD predictions without the need to repeatedly solve quantum…

机器学习 · 计算机科学 2026-04-24 Luke Thompson , Davy Guan , Dai Shi , Slade Matthews , Junbin Gao , Andi Han

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…

化学物理 · 物理学 2018-12-20 Michael Gastegger , Philipp Marquetand

Molecular Dynamics (MD) simulations are vital for exploring complex systems in computational physics and chemistry. While machine learning methods dramatically reduce computational costs relative to ab initio methods, their accuracy in…

材料科学 · 物理学 2025-07-18 Ivan Žugec , Tin Hadži Veljković , Maite Alducin , J. Iñaki Juaristi

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…

化学物理 · 物理学 2018-09-26 Stefan Chmiela , Huziel E. Sauceda , Klaus-Robert Müller , Alexandre Tkatchenko

Molecular dynamics (MD) simulates the time evolution of atomic systems governed by interatomic forces, and the fidelity of these simulations depends critically on the underlying force model. Classical force fields (CFFs) rely on fixed…

Accurate and efficient simulation of infrared (IR) and Raman spectra is essential for molecular identification and structural analysis. Traditional quantum chemistry methods based on the harmonic approximation neglect anharmonicity and…

化学物理 · 物理学 2025-10-07 Shengjiao Ji , Yujin Zhang , Zihan Zou , Bin Jiang , Jun Jiang , Yi Luo , Wei Hu

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.…

机器学习 · 计算机科学 2022-04-27 Zijie Li , Kazem Meidani , Prakarsh Yadav , Amir Barati Farimani

In drug discovery, molecular dynamics (MD) simulation for protein-ligand binding provides a powerful tool for predicting binding affinities, estimating transport properties, and exploring pocket sites. There has been a long history of…

Efficient molecular dynamics (MD) simulation is vital for understanding atomic-scale processes in materials science and biophysics. Traditional density functional theory (DFT) methods are computationally expensive, which limits the…

机器学习 · 计算机科学 2025-10-03 Hung Le , Sherif Abbas , Minh Hoang Nguyen , Van Dai Do , Huu Hiep Nguyen , Dung Nguyen

Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…

生物大分子 · 定量生物学 2026-04-21 Ziyang Yu , Wenbing Huang , Yang Liu
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