A force field as accurate as quantum mechanics (QMs) and as fast as molecular mechanics (MMs), with which one can simulate a biomolecular system efficiently enough and meaningfully enough to get quantitative insights, is among the most ardent dreams of biophysicists—a dream, nevertheless, not to be fulfilled any time soon. Machine learning force fields (MLFFs) represent a meaningful endeavor in this direction, where differentiable neural functions are parametrized to fit ab initio energies and forces through automatic differentiation. We argue that, as of now, the utility of the MLFF models is no longer bottlenecked by accuracy but primarily by their speed, as well as stability and generalizability—many recent variants, on limited chemical spaces, have long surpassed the chemical accuracy of 1 kcal/mol—the empirical threshold beyond which realistic chemical predictions are possible—though still magnitudes slower than MM. Hoping to kindle exploration and design of faster, albeit perhaps slightly less accurate MLFFs, in this review, we focus our attention on the technical design space (the speed-accuracy trade-off) between MM and ML force fields. After a brief review of the building blocks (from a machine learning-centric point of view) of force fields of either kind, we discuss the desired properties and challenges now faced by the force field development community, survey the efforts to make MM force fields more accurate and ML force fields faster, and envision what the next generation of MLFF might look like.
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June 2025
Review Article|
April 02 2025
On the design space between molecular mechanics and machine learning force fields
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Yuanqing Wang
;
Yuanqing Wang
a)
(Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing)
1
Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University
, New York, New York 10003, USA
2
Center for Data Science, New York University
, New York, New York 10004, USA
3
Courant Institute of Mathematical Sciences, New York University
, New York, New York 10003, USA
a)Author to whom correspondence should be addressed: [email protected]
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Kenichiro Takaba
;
Kenichiro Takaba
(Writing – original draft)
4
Asahi Kasei Pharma Corporation
, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
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Michael S. Chen;
Michael S. Chen
(Writing – original draft)
1
Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University
, New York, New York 10003, USA
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Marcus Wieder
;
Marcus Wieder
(Writing – original draft)
5
Open Molecular Software Foundation
, Davis, California 95616, USA
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Yuzhi Xu
;
Yuzhi Xu
(Writing – original draft)
1
Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University
, New York, New York 10003, USA
6
NYU-ECNU Center for Computational Chemistry and Shanghai Frontiers Science Center of Artificial Intelligence and Deep Learning, NYU Shanghai
, Shanghai 200062, People's Republic of China
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Tong Zhu
;
Tong Zhu
(Writing – original draft)
6
NYU-ECNU Center for Computational Chemistry and Shanghai Frontiers Science Center of Artificial Intelligence and Deep Learning, NYU Shanghai
, Shanghai 200062, People's Republic of China
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John Z. H. Zhang
;
John Z. H. Zhang
(Writing – original draft)
6
NYU-ECNU Center for Computational Chemistry and Shanghai Frontiers Science Center of Artificial Intelligence and Deep Learning, NYU Shanghai
, Shanghai 200062, People's Republic of China
7
Faculty of Synthetic Biology, Shenzhen University of Advanced Technology
, Shenzhen 518055, People's Republic of China
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Arnav Nagle;
Arnav Nagle
(Writing – original draft)
8
University of Washington
, Seattle, Washington 98195, USA
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Kuang Yu
;
Kuang Yu
(Writing – original draft)
9
Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University
, Shenzhen 518055, People's Republic of China
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Xinyan Wang
;
Xinyan Wang
(Writing – original draft)
10
DP Technology
, Beijing 100089, People's Republic of China
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Daniel J. Cole
;
Daniel J. Cole
(Writing – original draft)
11
School of Natural and Environmental Sciences, Newcastle University
, Newcastle upon Tyne NE1 7RU, United Kingdom
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Joshua A. Rackers
;
Joshua A. Rackers
(Writing – original draft)
12
Prescient Design, Genentech
, New York
, New York 10004, USA
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Kyunghyun Cho
;
Kyunghyun Cho
(Writing – original draft)
2
Center for Data Science, New York University
, New York, New York 10004, USA
3
Courant Institute of Mathematical Sciences, New York University
, New York, New York 10003, USA
12
Prescient Design, Genentech
, New York
, New York 10004, USA
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Joe G. Greener
;
Joe G. Greener
(Writing – original draft)
13
Medical Research Council Laboratory of Molecular Biology
, Cambridge CB2 0QH, United Kingdom
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Peter Eastman
;
Peter Eastman
(Writing – original draft)
14
Department of Chemistry, Stanford University
, Stanford, California 94305, USA
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Stefano Martiniani
;
Stefano Martiniani
(Writing – original draft)
1
Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University
, New York, New York 10003, USA
3
Courant Institute of Mathematical Sciences, New York University
, New York, New York 10003, USA
15
Center for Soft Matter Research, Department of Physics, New York University
, New York
, New York 10003, USA
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Mark E. Tuckerman
Mark E. Tuckerman
(Funding acquisition, Writing – original draft)
1
Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University
, New York, New York 10003, USA
3
Courant Institute of Mathematical Sciences, New York University
, New York, New York 10003, USA
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Yuanqing Wang
1,2,3,a)
Kenichiro Takaba
4
Michael S. Chen
1
Marcus Wieder
5
Yuzhi Xu
1,6
Tong Zhu
6
John Z. H. Zhang
6,7
Arnav Nagle
8
Kuang Yu
9
Xinyan Wang
10
Daniel J. Cole
11
Joshua A. Rackers
12
Kyunghyun Cho
2,3,12
Joe G. Greener
13
Peter Eastman
14
Stefano Martiniani
1,3,15
Mark E. Tuckerman
1,3
1
Simons Center for Computational Physical Chemistry, Department of Chemistry, New York University
, New York, New York 10003, USA
2
Center for Data Science, New York University
, New York, New York 10004, USA
3
Courant Institute of Mathematical Sciences, New York University
, New York, New York 10003, USA
4
Asahi Kasei Pharma Corporation
, 632-1 Mifuku, Izunokuni, Shizuoka 410-2321, Japan
5
Open Molecular Software Foundation
, Davis, California 95616, USA
6
NYU-ECNU Center for Computational Chemistry and Shanghai Frontiers Science Center of Artificial Intelligence and Deep Learning, NYU Shanghai
, Shanghai 200062, People's Republic of China
7
Faculty of Synthetic Biology, Shenzhen University of Advanced Technology
, Shenzhen 518055, People's Republic of China
8
University of Washington
, Seattle, Washington 98195, USA
9
Institute of Materials Research, Tsinghua Shenzhen International Graduate School, Tsinghua University
, Shenzhen 518055, People's Republic of China
10
DP Technology
, Beijing 100089, People's Republic of China
11
School of Natural and Environmental Sciences, Newcastle University
, Newcastle upon Tyne NE1 7RU, United Kingdom
12
Prescient Design, Genentech
, New York
, New York 10004, USA
13
Medical Research Council Laboratory of Molecular Biology
, Cambridge CB2 0QH, United Kingdom
14
Department of Chemistry, Stanford University
, Stanford, California 94305, USA
15
Center for Soft Matter Research, Department of Physics, New York University
, New York
, New York 10003, USA
a)Author to whom correspondence should be addressed: [email protected]
Appl. Phys. Rev. 12, 021304 (2025)
Article history
Received:
September 07 2024
Accepted:
March 18 2025
Citation
Yuanqing Wang, Kenichiro Takaba, Michael S. Chen, Marcus Wieder, Yuzhi Xu, Tong Zhu, John Z. H. Zhang, Arnav Nagle, Kuang Yu, Xinyan Wang, Daniel J. Cole, Joshua A. Rackers, Kyunghyun Cho, Joe G. Greener, Peter Eastman, Stefano Martiniani, Mark E. Tuckerman; On the design space between molecular mechanics and machine learning force fields. Appl. Phys. Rev. 1 June 2025; 12 (2): 021304. https://doi.org/10.1063/5.0237876
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