ArticleJournal of computational chemistry2025
A Robust and Versatile QM/MM Interface for Molecular Dynamics in GROMOS.
Article in Journal of computational chemistry, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
1 citing paper in PubMed.
- Neural Network Potential with Multiresolution Approach Enables Accurate Prediction of Reaction Free Energies in Solution.Journal of the American Chemical Society · 2025Article
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Authors and funding
5 authors.
Funding
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 interface or the MD program itself. The improved QM/MM interface enables more advanced investigations into biomolecular reactivity, enzyme catalysis, and other phenomena requiring detailed quantum mechanical treatment within classical simulations. This work represents a significant advancement in the capabilities of GROMOS, providing enhanced tools to explore complex molecular systems.
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Registered trials
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