2024/11/12 by Ivan Gilardoni, Valerio Piomponi, Thorben Fröhlking +1 · 2 voices · 2 citations
Biochemistry, Genetics and Molecular Biology · Mathematics · Physics and Astronomy · #Advanced Chemical Physics Studies #Artificial intelligence #Benchmark (surveying) #Computational science #Computer science #Field (mathematics) #Force field (fiction) #Mathematics #Molecular dynamics #Observable #Open source #Physics #Programming language #Protein Structure and Dynamics #Python (programming language) #Software #Source code #Spectroscopy and Quantum Chemical Studies
paper · pdf · doi:10.1063/5.0256841
published in The Journal of Chemical Physics 162(19) (American Institute of Physics)
openalex publication_date 2025/05/15 · openalex created_date 2025/05/16 · openalex updated_date 2026/07/14
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce and predict dynamics in agreement with experiments is limited by the accuracy of the force-field model. This capability can be improved by refining the structural ensembles or the force-field parameters. Furthermore, discrepancies with experimental data can be due to imprecise forward models, namely, functions mapping simulated structures to experimental observables. Here, we introduce MDRefine, a Python package aimed at implementing the refinement of the ensemble, the force field, and/or the forward model by comparing MD-generated trajectories with the experimental data. The software consists of several tools that can be employed separately from each other or combined together in different ways, providing a seamless interpolation between these three different types of refinement. We use some benchmark cases to show that the combined approach is superior to separately applied refinements. MDRefine has been released as an open-source package under the LGPLv2+ license. Source code, documentation, and examples are available at https://pypi.org/project/MDRefine and https://github.com/bussilab/MDRefine.