MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data

TL;DR

MDRefine is a versatile Python package that improves molecular dynamics simulations by refining ensembles, force-fields, and forward models through comparison with experimental data, enhancing the accuracy of conformational predictions.

Contribution

It introduces a flexible software tool that integrates multiple refinement strategies for MD simulations, which was not previously available in a unified package.

Findings

Combined refinement approach outperforms individual methods

Software is modular and easy to use

Benchmark results demonstrate improved accuracy

Abstract

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 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. Source code, documentation and examples are freely available at https://pypi.org/project/MDRefine and https://github.com/bussilab/MDRefine.