Using collective variables to drive molecular dynamics simulations
Open accessAbstract
A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.
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The geometrical route has been automated with quaternion-based angle restraints as CVs in the NAMD and GROMACS MD engines.
“The geometrical route has been automated with quaternion-based angle restraints67 as CVs in the NAMD70,71 and GROMACS72 MD engines.”
From Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints (2025) · cites this paper as [71]
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Structural basis of template strand deoxyuridine promoter recognition by a viral RNA polymerase
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- Authors
- Fiorin, G., Klein, M. L., & Hénin, J.
- Affiliations
- Temple University (US)
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Fiorin, Giacomo
- Venue
- Molecular Physics
- Publisher
- Informa UK Limited
- Published
- 2013-12
- Volume
- 111
- Issue
- 22-23
- Pages
- 3345-3362
- ISSN
- 0026-8976 (ISSN-L)
- 1362-3028
- OpenAlex
- W2058971275
- Cited by
- 1,053
- References
- 2
- Citations by year
- 2026: 113 · 2025: 121 · 2024: 108 · 2023: 115 · 2022: 124 · 2021: 97 · 2020: 83 · 2019: 80 · 2018: 83 · 2017: 46 · 2016: 36 · 2015: 22 · 2014: 20 · 2013: 4
- FWCI
- 17.29
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Physics (publishedVersion, cc-by)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion, cc-by)
- HAL (submittedVersion)
- Funders
- National Science Foundation (CHE-1212416)
- Topics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Physics and Astronomy › Atomic and Molecular Physics, and Optics › Advanced Chemical Physics Studies
- Keywords
- collective variables, steered molecular dynamics, targeted molecular dynamics, metadynamics, adaptive biasing force, free energy calculation, modular simulation framework
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