Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
Abstract
Atomic motions in molecules are not linear. This infers that nonlinear dimensionality reduction methods can outperform linear ones in analysis of collective atomic motions. In addition, nonlinear collective motions can be used as potentially efficient guides for biased simulation techniques. Here we present a simulation with a bias potential acting in the directions of collective motions determined by a nonlinear dimensionality reduction method. Ad hoc generated conformations of trans,trans-1,2,4-trifluorocyclooctane were analyzed by Isomap method to map these 72-dimensional coordinates to three dimensions, as described by Brown and co-workers [J. Chem. Phys. 129, 064118 (2008)]. Metadynamics employing the three-dimensional embeddings as collective variables was applied to explore all relevant conformations of the studied system and to calculate its conformational free energy surface. The method sampled all relevant conformations (boat, boat-chair, and crown) and corresponding transition structures inaccessible by an unbiased simulation. This scheme allows to use essentially any parameter of the system as a collective variable in biased simulations. Moreover, the scheme we used for mapping out-of-sample conformations from the 72D to 3D space can be used as a general purpose mapping for dimensionality reduction, beyond the context of molecular modeling.
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The challenge of identifying the most appropriate low-dimensional space to accelerate conformational sampling is reflected in the fact that most early (and recent) applications of dimensionality reduction to atomistic modeling involved simulations of rare events or phase transitions.
“The challenge of identifying the most appropriate low-dimensional space to accelerate conformational sampling is reflected in the fact that most of early (and recent) applications of dimensionality reduction to atomistic modeling involved simulations of rare events or phase transitions 71,72,95-98 .”
From Unsupervised machine learning in atomistic simulations, between predictions and understanding (2019) · cites this paper as [96]
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- Authors
- Spiwok, V., & Králová, B.
- Affiliations
- Institute of Chemistry of the Slovak Academy of Sciences (SK)
- University of Chemistry and Technology, Prague (CZ)
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2011-12-08
- Volume
- 135
- Issue
- 22
- Pages
- 224504-224504
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W2051629080
- Cited by
- 70
- References
- 38
- Citations by year
- 2026: 2 · 2025: 3 · 2024: 3 · 2023: 1 · 2022: 12 · 2021: 3 · 2020: 5 · 2019: 7 · 2018: 9 · 2017: 4 · 2016: 2 · 2015: 4 · 2014: 4 · 2013: 6 · 2012: 4
- FWCI
- 3.18
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- The Journal of Chemical Physics (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Slovenská Akadémia Vied
- Vedecká Grantová Agentúra MŠVVaŠ SR a SAV
- 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
- metadynamics, Isomap, nonlinear dimensionality reduction, collective atomic motion, conformational change
- MeSH terms
- Algorithms, Molecular Conformation, Motion, Thermodynamics, Nonlinear Dynamics, Molecular Dynamics Simulation
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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