Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration.
| Title: | Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration. |
|---|---|
| Authors: | Pasarkar, Amey P., Bencomo, Gianluca M., Olsson, Simon, Dieng, Adji Bousso |
| Source: | Journal of Chemical Physics; 10/14/2023, Vol. 159 Issue 14, p1-11, 11p |
| Subject Terms: | MOLECULAR conformation, METASTABLE states, MOLECULAR dynamics, STATISTICAL sampling, SAMPLING (Process) |
| Abstract: | Molecular dynamics (MD) is the method of choice for understanding the structure, function, and interactions of molecules. However, MD simulations are limited by the strong metastability of many molecules, which traps them in a single conformation basin for an extended amount of time. Enhanced sampling techniques, such as metadynamics and replica exchange, have been developed to overcome this limitation and accelerate the exploration of complex free energy landscapes. In this paper, we propose Vendi Sampling, a replica-based algorithm for increasing the efficiency and efficacy of the exploration of molecular conformation spaces. In Vendi sampling, replicas are simulated in parallel and coupled via a global statistical measure, the Vendi Score, to enhance diversity. Vendi sampling allows for the recovery of unbiased sampling statistics and dramatically improves sampling efficiency. We demonstrate the effectiveness of Vendi sampling in improving molecular dynamics simulations by showing significant improvements in coverage and mixing between metastable states and convergence of free energy estimates for four common benchmarks, including Alanine Dipeptide and Chignolin. [ABSTRACT FROM AUTHOR] |
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| Database: | Complementary Index |
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| Items | – Name: Title Label: Title Group: Ti Data: Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Pasarkar%2C+Amey+P%2E%22">Pasarkar, Amey P.</searchLink><br /><searchLink fieldCode="AR" term="%22Bencomo%2C+Gianluca+M%2E%22">Bencomo, Gianluca M.</searchLink><br /><searchLink fieldCode="AR" term="%22Olsson%2C+Simon%22">Olsson, Simon</searchLink><br /><searchLink fieldCode="AR" term="%22Dieng%2C+Adji+Bousso%22">Dieng, Adji Bousso</searchLink> – Name: TitleSource Label: Source Group: Src Data: Journal of Chemical Physics; 10/14/2023, Vol. 159 Issue 14, p1-11, 11p – Name: Subject Label: Subject Terms Group: Su Data: <searchLink fieldCode="DE" term="%22MOLECULAR+conformation%22">MOLECULAR conformation</searchLink><br /><searchLink fieldCode="DE" term="%22METASTABLE+states%22">METASTABLE states</searchLink><br /><searchLink fieldCode="DE" term="%22MOLECULAR+dynamics%22">MOLECULAR dynamics</searchLink><br /><searchLink fieldCode="DE" term="%22STATISTICAL+sampling%22">STATISTICAL sampling</searchLink><br /><searchLink fieldCode="DE" term="%22SAMPLING+%28Process%29%22">SAMPLING (Process)</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Molecular dynamics (MD) is the method of choice for understanding the structure, function, and interactions of molecules. However, MD simulations are limited by the strong metastability of many molecules, which traps them in a single conformation basin for an extended amount of time. Enhanced sampling techniques, such as metadynamics and replica exchange, have been developed to overcome this limitation and accelerate the exploration of complex free energy landscapes. In this paper, we propose Vendi Sampling, a replica-based algorithm for increasing the efficiency and efficacy of the exploration of molecular conformation spaces. In Vendi sampling, replicas are simulated in parallel and coupled via a global statistical measure, the Vendi Score, to enhance diversity. Vendi sampling allows for the recovery of unbiased sampling statistics and dramatically improves sampling efficiency. We demonstrate the effectiveness of Vendi sampling in improving molecular dynamics simulations by showing significant improvements in coverage and mixing between metastable states and convergence of free energy estimates for four common benchmarks, including Alanine Dipeptide and Chignolin. [ABSTRACT FROM AUTHOR] – Name: Abstract Label: Group: Ab Data: <i>Copyright of Journal of Chemical Physics is the property of American Institute of Physics and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1063/5.0166172 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 11 StartPage: 1 Subjects: – SubjectFull: MOLECULAR conformation Type: general – SubjectFull: METASTABLE states Type: general – SubjectFull: MOLECULAR dynamics Type: general – SubjectFull: STATISTICAL sampling Type: general – SubjectFull: SAMPLING (Process) Type: general Titles: – TitleFull: Vendi sampling for molecular simulations: Diversity as a force for faster convergence and better exploration. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Pasarkar, Amey P. – PersonEntity: Name: NameFull: Bencomo, Gianluca M. – PersonEntity: Name: NameFull: Olsson, Simon – PersonEntity: Name: NameFull: Dieng, Adji Bousso IsPartOfRelationships: – BibEntity: Dates: – D: 14 M: 10 Text: 10/14/2023 Type: published Y: 2023 Identifiers: – Type: issn-print Value: 00219606 Numbering: – Type: volume Value: 159 – Type: issue Value: 14 Titles: – TitleFull: Journal of Chemical Physics Type: main |
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