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From gHBfix to NBfix: Reweighting-Driven Refinement of Hydrogen-Bond Interactions in RNA Force Fields

Mlýnský, Vojtěch
•
Kührová, Petra
•
Bussi, Giovanni
altro
Banáš, Pavel
2026
  • journal article

Periodico
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
Abstract
Understanding RNA structural dynamics is essential for elucidating its biological functions, and molecular dynamics (MD) simulations provide an important atomistic complement to experimental approaches. However, the predictive power of MD is fundamentally limited by the accuracy of the underlying empirical force fields (FFs), particularly in capturing the delicate balance of nonbonded interactions. Here, we present a systematic reparameterization strategy that replaces the external gHBfix19 hydrogen-bond (H-bond) correction potential with an equivalent and easy-to-use NBfix Lennard-Jones representation of its main thermodynamic effects within the state-of-the-art OL3 RNA FF. Using a quantitatively converged temperature replica-exchange MD ensemble of the GAGA tetraloop, we employed a reweighting-based optimization protocol to derive NBfix parameters that reproduce the thermodynamic effects of the original gHBfix19 terms. Sequential optimization of the individual gHBfix19 components proved essential to ensure stable and transferable parameter refinement. The resulting fully reformulated NBfix-based variant, termed OL3CP-NBfix19, was validated on a representative set of RNA motifs, including tetranucleotides, A-form duplexes, and tetraloops. Across all tested systems, its performance is comparable to that of the reference gHBfix19 FF. By embedding the H-bond corrections directly into the standard nonbonded framework, the NBfix formulation eliminates external biasing potentials, simplifies practical deployment, and reduces computational overhead. Beyond this specific reparameterization, our results demonstrate a practical workflow for translating targeted H-bond corrections into native FF terms for efficient biomolecular simulations.
DOI
10.1021/acs.jctc.6c00924
WOS
WOS:001852484600001
Archivio
https://hdl.handle.net/20.500.11767/152550
https://www.biorxiv.org/content/10.64898/2026.03.20.713292v1
https://ricerca.unityfvg.it/handle/20.500.11767/152550
Diritti
open access
license:creative commons
license uri:http://creativecommons.org/licenses/by/4.0/
Soggetti
  • Settore PHYS-04/A - F...

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