A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS.

ABSTRACT: The integration of quantum mechanics and molecular mechanics (QM/MM) within molecular dynamics simulations is crucial to accurately model complex biochemical systems. Here, we present an enhanced implementation of the QM/MM interface in the GROMOS simulation package, introducing significant improvements in functionality and user control. We present new features, including the link atom scheme, which allows the modeling of QM regions as a part of bigger molecules. Benchmark tests on various systems, including QM water in water, amino acids in water, and tripeptides validate the reliability of the new functionalities. Performance evaluations demonstrate that the updated implementation is efficient, with the primary computational burden attributed to the QM program rather than the QM/MM inter

SUBMITTER: Poliak P 

PROVIDER: S-EPMC11804165 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature