3 papers
physics.chem-ph2026
Bayesian Sampling of Structural Ensembles: The Role of Ensemble-Counting Measures
Ivan Gilardoni, Giovanni Bussi
Structural ensemble refinement is widely used to integrate molecular simulations with experimental measurements. While most applications focus on the maximum-a-posteriori (MAP) ens…
physics.chem-ph2024
MDRefine: a Python package for refining Molecular Dynamics trajectories with experimental data
Ivan Gilardoni, Valerio Piomponi, Thorben Fröhlking +1
Molecular dynamics (MD) simulations play a crucial role in resolving the underlying conformational dynamics of molecular systems. However, their capability to correctly reproduce a…
physics.chem-ph2023
Boosting ensemble refinement with transferable force field corrections: synergistic optimization for molecular simulations
Ivan Gilardoni, Thorben Fröhlking, Giovanni Bussi
A novel method combining the ensemble refinement by maximum entropy principle and the force field fitting approach is presented. Its formulation allows to continuously interpolate…