Evidence map›Paper›PMID 37526163›Full record

ArticleThe Journal of chemical physics2023

DeePMD-kit v2: A software package for deep potential models.

Jinzhe Zeng, Duo Zhang, Denghui Lu, Pinghui Mo, Zeyu Li, Yixiao Chen, Marián Rynik, Li'ang Huang, Ziyao Li, Shaochen Shi and 37 more

Abstract read
In one paragraph

Article in The Journal of chemical physics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 96 papers.

0numbers the graph read from it
0cells of the map it votes in
96citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

96 citing papers in PubMed.

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  20. Direction-specific enhanced diffusion of CONature communications · 2026
    Article

36 more citing papers are in PubMed but not listed here.

4 · The record

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5 · Who and what money

Authors and funding

47 authors.

Jinzhe ZengLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.ORCID 0000-0002-1515-8172
Duo ZhangAI for Science Institute, Beijing 100080, People's Republic of China.ORCID 0000-0001-9591-2659
Denghui LuHEDPS, CAPT, College of Engineering, Peking University, Beijing 100871, People's Republic of China.ORCID 0000-0003-0977-3635
Pinghui MoCollege of Electrical and Information Engineering, Hunan University, Changsha, People's Republic of China.ORCID 0009-0009-4591-8644
Zeyu LiYuanpei College, Peking University, Beijing 100871, People's Republic of China.ORCID 0009-0008-4381-0544
Yixiao ChenProgram in Applied and Computational Mathematics, Princeton University, Princeton, New Jersey 08540, USA.ORCID 0000-0001-8201-5887
Marián RynikDepartment of Experimental Physics, Comenius University, Mlynská Dolina F2, 842 48 Bratislava, Slovakia.ORCID 0009-0006-5745-1525
Li'ang HuangCenter for Quantum Information, Institute for Interdisciplinary Information Sciences, Tsinghua University, Beijing 100084, People's Republic of China.ORCID 0009-0001-4185-9677
Ziyao LiLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.ORCID 0000-0002-9071-2516
Shaochen ShiByteDance Research, Zhonghang Plaza, No. 43, North 3rd Ring West Road, Haidian District, Beijing, People's Republic of China.ORCID 0000-0003-3457-403X
Yingze WangLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.
Haotian YeYuanpei College, Peking University, Beijing 100871, People's Republic of China.ORCID 0009-0005-8486-0626
Ping TuoAI for Science Institute, Beijing 100080, People's Republic of China.ORCID 0000-0002-6477-5900
Jiabin YangBaidu, Inc., Beijing, People's Republic of China.
Ye DingLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.ORCID 0009-0005-1986-2879
Yifan LiDepartment of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.ORCID 0000-0003-3217-0592
Davide TisiLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.ORCID 0000-0001-7229-6101
Qiyu ZengDepartment of Physics, National University of Defense Technology, Changsha, Hunan 410073, People's Republic of China.ORCID 0009-0004-2304-0213
Han BaoAI for Science Institute, Beijing 100080, People's Republic of China.ORCID 0000-0003-3490-0974
Yu XiaByteDance Research, Zhonghang Plaza, No. 43, North 3rd Ring West Road, Haidian District, Beijing, People's Republic of China.ORCID 0009-0004-9087-9414
Jiameng HuangAI for Science Institute, Beijing 100080, People's Republic of China.ORCID 0009-0002-9701-8145
Koki MuraokaDepartment of Chemical System Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.ORCID 0000-0003-1830-7978
Yibo WangDP Technology, Beijing 100080, People's Republic of China.ORCID 0009-0001-3921-4415
Junhan ChangLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.ORCID 0000-0003-3195-0773
Fengbo YuanDP Technology, Beijing 100080, People's Republic of China.ORCID 0009-0002-3949-8785
Sigbjørn Løland BoreHylleraas Centre for Quantum Molecular Sciences and Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, 0315 Oslo, Norway.ORCID 0000-0002-8620-4885
Chun CaiAI for Science Institute, Beijing 100080, People's Republic of China.ORCID 0000-0001-6242-0439
Yinnian LinWangxuan Institute of Computer Technology, Peking University, Beijing 100871, People's Republic of China.ORCID 0009-0008-1709-7239
Bo WangShanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry and Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, People's Republic of China.ORCID 0000-0002-2733-9253
Jiayan XuSchool of Chemistry and Chemical Engineering, Queen's University Belfast, Belfast BT9 5AG, United Kingdom.ORCID 0000-0001-9897-5778
Jia-Xin ZhuState Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China.ORCID 0000-0002-3471-4728
Chenxing LuoDepartment of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, USA.ORCID 0000-0003-4116-6851
Yuzhi ZhangDP Technology, Beijing 100080, People's Republic of China.ORCID 0000-0002-5841-1107
Rhys E A GoodallIndependent Researcher, London, United Kingdom.ORCID 0000-0002-6589-1700
Wenshuo LiangDP Technology, Beijing 100080, People's Republic of China.ORCID 0000-0003-0646-8803
Anurag Kumar SinghDepartment of Data Science, Indian Institute of Technology, Palakkad, Kerala, India.ORCID 0009-0001-6255-5867
Sikai YaoDP Technology, Beijing 100080, People's Republic of China.ORCID 0009-0009-3429-0476
Jingchao ZhangNVIDIA AI Technology Center (NVAITC), Santa Clara, California 95051, USA.ORCID 0000-0001-5289-6062
Renata WentzcovitchDP Technology, Beijing 100080, People's Republic of China.ORCID 0000-0001-5663-9426
Jiequn HanCenter for Computational Mathematics, Flatiron Institute, New York, New York 10010, USA.ORCID 0000-0002-3553-7313
Jie LiuCollege of Electrical and Information Engineering, Hunan University, Changsha, People's Republic of China.ORCID 0000-0001-8663-3551
Weile JiaAI for Science Institute, Beijing 100080, People's Republic of China.ORCID 0000-0001-8539-8326
Darrin M YorkLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.ORCID 0000-0002-9193-7055
Weinan EAI for Science Institute, Beijing 100080, People's Republic of China.ORCID 0000-0003-0272-9500
Roberto CarDepartment of Chemistry, Princeton University, Princeton, New Jersey 08544, USA.ORCID 0000-0001-5243-2647
Linfeng ZhangAI for Science Institute, Beijing 100080, People's Republic of China.ORCID 0000-0002-8470-5846
Han WangDP Technology, Beijing 100080, People's Republic of China.ORCID 0000-0001-5623-1148

Funding

Next-generation integrated quantum force fields for biomedical applicationsR01GM107485 · NIGMS · RUTGERS, THE STATE UNIV OF N.J. · PI Darrin M York · 2015 to 2026
$3.8M
NIGMS NIH HHS R01 GM107485
6 · The paper itself

Abstract

DeePMD-kit is a powerful open-source software package that facilitates molecular dynamics simulations using machine learning potentials known as Deep Potential (DP) models. This package, which was released in 2017, has been widely used in the fields of physics, chemistry, biology, and material science for studying atomistic systems. The current version of DeePMD-kit offers numerous advanced features, such as DeepPot-SE, attention-based and hybrid descriptors, the ability to fit tensile properties, type embedding, model deviation, DP-range correction, DP long range, graphics processing unit support for customized operators, model compression, non-von Neumann molecular dynamics, and improved usability, including documentation, compiled binary packages, graphical user interfaces, and application programming interfaces. This article presents an overview of the current major version of the DeePMD-kit package, highlighting its features and technical details. Additionally, this article presents a comprehensive procedure for conducting molecular dynamics as a representative application, benchmarks the accuracy and efficiency of different models, and discusses ongoing developments.

Identifiers

PMID37526163
PMCPMC10445636

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.