Probability Density Reweighting of High-Temperature Molecular Dynamics.
J Chem Theory Comput
; 20(12): 4977-4985, 2024 Jun 25.
Article
en En
| MEDLINE
| ID: mdl-38758038
ABSTRACT
Molecular dynamics (MD) simulation is a popular method for elucidating the structures and functions of biomolecules. However, exploring the conformational space, especially for large systems with slow transitions, often requires enhanced sampling methods. Although conducting MD at high temperatures provides a straightforward approach, resulting conformational ensembles diverge significantly from those at low temperatures. To address this discrepancy, we propose a novel probability density-based reweighting (PDR) method. PDR exhibits robust performance across four distinct systems, including a miniprotein, a cyclic peptide, a protein loop, and a protein-peptide complex. It accurately restores the conformational distributions at high temperatures to those at low temperatures. Additionally, we apply PDR to reweight previously studied high-T MD simulations of 12 protein-peptide complexes, enabling a comprehensive investigation of the conformational space of protein-peptide complexes.
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1
Colección:
01-internacional
Base de datos:
MEDLINE
Idioma:
En
Revista:
J Chem Theory Comput
Año:
2024
Tipo del documento:
Article
País de afiliación:
China
Pais de publicación:
Estados Unidos