The Effects of Conformational Sampling and QM Region Size in QM/MM Simulations: An Adaptive QM/MM Study With Model Systems.

ABSTRACT: Molecular properties in combined quantum mechanics and molecular mechanics (QM/MM) simulations have been shown to be dependent on the size of the quantum mechanical (QM) region and the amount of conformational sampling. Previous studies have largely focused on enzymatic systems, which have made it difficult to distinguish the effects of QM region size and conformational sampling from other factors including QM-MM boundary artifacts and the boundary effects. This study uses the difference-based adaptive solvation QM/MM method to investigate the tautomerization reactions of alanine and aspartate in explicit solvent. The choice of computationally tractable systems enables the decoupling of QM region size effects from other factors and a direct comparison of free energy surfaces with potential

SUBMITTER: Paz H 

PROVIDER: S-EPMC12008714 | biostudies-literature | 2025 Apr

REPOSITORIES: biostudies-literature