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bioRxiv · 10.1101/2025.06.14.659665

Enhanced Sampling on Domain/Motif Level with Kinetic Accelerated Molecular Dynamics

Wei, H.
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Abstract

Molecular dynamics (MD) has become a popular simulation tool in recent years. However, its application is often limited by a timescale problem, due to its femtosecond-level integration timestep. To address this challenge, various enhanced sampling methods have been developed to accelerate system dynamics. Here, we introduce a novel enhanced sampling approach: Kinetically Accelerated Molecular Dynamics (KAMD). By combining the atomic-level accuracy of MD with the diffusive behavior of Brownian dynamics (BD), KAMD significantly improves sampling efficiency on domain/motif level while preserving equilibrium properties. We showed that KAMD is particularly effective in simulating two types of processes: large-scale conformational changes and ligand unbinding events.

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Wei, H.. 2025-06-14. Enhanced Sampling on Domain/Motif Level with Kinetic Accelerated Molecular Dynamics. https://doi.org/10.1101/2025.06.14.659665

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