SAXS-Guided Metadynamics
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Updated: Mar 30, 2026

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
Published on: August 9, 2024
Dari Kimanius1, Ingrid Pettersson2, Gerd Schluckebier2
1Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University , SE-106 91 Stockholm, Sweden.
Abstract:
The small-angle X-ray scattering (SAXS) methodology enables structural characterization of biological macromolecules in solution. However, because SAXS provides low-dimensional information, several potential structural configurations can reproduce the experimental scattering profile, which severely complicates the structural refinement process. Here, we present a bias-exchange metadynamics refinement protocol that incorporates SAXS data as collective variables and therefore tags all possible configurations with their corresponding free energies, which allows identification of a unique structural solution. The method has been implemented in PLUMED and combined with the GROMACS simulation package, and as a proof of principle, we explore the Trp-cage protein folding landscape.
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