Generation of conformational ensembles of small molecules via surrogate model-assisted molecular dynamics

Abstract

The accurate prediction of thermodynamic properties is crucial in various fields such as drug discovery and materials design. This task relies on sampling from the underlying Boltzmann distribution, which is challenging using conventional approaches such as simulations. In this work, we introduce surrogate model-assisted molecular dynamics (SMA-MD), a new procedure to sample the equilibrium ensemble of molecules. First, SMA-MD leverages deep generative models to enhance the sampling of slow degrees of freedom. Subsequently, the generated ensemble undergoes statistical reweighting, followed by short simulations. Our empirical results show that SMA-MD generates more diverse and lower energy ensembles than conventional MD simulations. Furthermore, we showcase the application of SMA-MD for the computation of thermodynamical properties by estimating implicit solvation free energies.

Keywords

• generative models
• Boltzmann distribution
• molecular conformation generation
• molecular dynamics
• property prediction
• equilibrium sampling