Neural Network-Based Molecular Dynamics Simulation of Water Assisted by Active Learning

In our study, we combined classical molecular dynamics (MD) simulations with the simulated annealing (SA) method to explore the conformational landscape of water molecules. By using the <i>K</i>-means clustering method, we processed the MD simulation data to extract representative samples of water molecular structures used to train a deep potential (DP) model. Our DeePMD method showed accuracy in predicting water structural properties compared to DFT-MD results. Meanwhile, this approach achieves a balanced prediction of water density and self-diffusion coefficients compared with earlier DeePMD simulations. These results highlight the essential role of representative sampling techniques in training the DP model. Furthermore, we demonstrated the effectiveness of combining the DeePMD simulation with the centroid molecular dynamics (CMD) approach, which incorporates nuclear quantum effects (NQEs). This approach successfully reproduced the shoulder feature at 3250 cm<sup>-1</sup> in the Raman spectra for the O-H stretch. Incorporating the path integral method into the DeePMD simulations underscores the importance of considering NQEs in understanding water molecules' structural and dynamic behaviors.

Authors

Institutions

Publication Details

Journal
The Journal of Physical Chemistry B
Published
2025-04-03
DOI
https://doi.org/10.1021/acs.jpcb.4c06633
Citations
3
Primary Topic
Spectroscopy and Quantum Chemical Studies
Type
article
Field-Weighted Citation Impact
3.74

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Neural Network-Based Molecular Dynamics Simulation of Water Assisted by Active Learning

Hujun Shen, Dan Zhao, Yao Huang
3 citations
The Journal of Physical Chemistry B
Spectroscopy and Quantum Chemical Studies
3.74
article

Neural Network-Based Molecular Dynamics Simulation of Water Assisted by Active Learning

Hujun Shen, Dan Zhao, Yao Huang
article en
3 citations

Abstract

In our study, we combined classical molecular dynamics (MD) simulations with the simulated annealing (SA) method to explore the conformational landscape of water molecules. By using the <i>K</i>-means clustering method, we processed the MD simulation data to extract representative samples of water molecular structures used to train a deep potential (DP) model. Our DeePMD method showed accuracy in predicting water structural properties compared to DFT-MD results. Meanwhile, this approach achieves a balanced prediction of water density and self-diffusion coefficients compared with earlier DeePMD simulations. These results highlight the essential role of representative sampling techniques in training the DP model. Furthermore, we demonstrated the effectiveness of combining the DeePMD simulation with the centroid molecular dynamics (CMD) approach, which incorporates nuclear quantum effects (NQEs). This approach successfully reproduced the shoulder feature at 3250 cm<sup>-1</sup> in the Raman spectra for the O-H stretch. Incorporating the path integral method into the DeePMD simulations underscores the importance of considering NQEs in understanding water molecules' structural and dynamic behaviors.

The Journal of Physical Chemistry BVol. 129(15)
Guizhou University of Finance and Economics (CN), Guizhou Education University (CN)
Guizhou Education University, National Natural Science Foundation of China, Guizhou University of Finance and Economics
Clean water and sanitation
Openalex Percentile: Top 8%
Spectroscopy and Quantum Chemical Studies
3.74
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.

Neural Network-Based Molecular Dynamics Simulation of Water Assisted by Active Learning — Hujun Shen, Dan Zhao, et al. · The Journal of Physical Chemistry B (2025) | TGRS Research Map | TGRS