Related Experiment Video
Updated: Mar 16, 2026

Multiscale Sampling of a Heterogeneous Water/Metal Catalyst Interface using Density Functional Theory and Force-Field Molecular Dynamics
Published on: April 12, 2019
Practical Aspects of Multiscale Classical and Quantum Simulations of Enzyme Reactions
M Dixit1, S Das1, A R Mhashal1
1Lise Meitner-Minerva Center of Computational Quantum Chemistry, Bar-Ilan University, Ramat Gan, Israel.
Abstract:
This chapter aims to present some basic multiscale approaches available for enzyme simulations, and to point out practical details and pitfalls that are not often discussed in the literature, but can greatly influence the outcome of any in silico enzyme study. We cover principle methodological steps of multiscale studies of general enzyme reactions. This includes choice of starting structures, boundary conditions, potential energy surfaces, reaction coordinates, simulation methods, as well as the choice of method for the treatment of nuclear quantum effects. Together, these and additional steps are crucial for the success of enzyme-modeling projects and should be considered prior to embarking on multiscale modeling.
More Related Videos
07:31Author Spotlight: Advancing Cell Membrane Biophysics - Exploring Interactions and Challenges Through Experimental and Computational Approaches
Published on: September 1, 2023
09:42Unraveling Entropic Rate Acceleration Induced by Solvent Dynamics in Membrane Enzymes
Published on: January 16, 2016
Related Concept Videos
Introduction to Mechanisms of Enzyme Catalysis
Introduction to Enzyme Kinetics
The experimenter can then plot the initial reaction rate or velocity (Vo) of a given trial against the substrate concentration ([S]) to obtain a graph of the reaction properties. For many enzymatic reactions involving a...
Enzyme Kinetics
Scientists typically study enzyme kinetics with a fixed amount of enzyme in the controlled environment of a test tube. When more reactant, or substrate, is...
Reaction Mechanisms: Rate-limiting Step Approximation
Multi-Step Reactions