A simple, step-by-step tutorial on how to load a basic MM system (blocked alanine - bALA), perform geometry optimization, and scan a simple reaction coordinate.

In this tutorial, we will model a simple SN2 reaction through a relaxed scan, using a semiempirical quantum chemistry potential and applying multiple distance restraints.

In this tutorial, we will model a classical Diels–Alder reaction by performing a relaxed scan along two simple reaction coordinates simultaneously, using a semiempirical quantum chemistry potential. The goal is to explore the two-dimensional potential energy landscape.

In this tutorial, we will run a short equilibrium molecular dynamics simulation and analyze the results using EasyHybrid’s tools for visualization and basic system analysis.

This tutorial demonstrates the use of the NEB method to investigate the interconversion between the chair and twist-boat conformations of cyclohexane. This approach enables the identification of the minimum energy path and estimation of the conformational barrier.

This tutorial demonstrates how to define a quantum (QM) region in a system previously prepared with the OPLS force field, creating a QM/MM hybrid Hamiltonian. It also shows how to perform a geometry optimization and visualize molecular orbitals for the optimized structure.

In this tutorial, we will revisit the hydrogen bond in the bAla system, this time calculating the reaction free energy using the umbrella sampling technique.

In this tutorial, we will model the catalytic degradation of 1-chlorobutane by the haloalkane dehalogenase LinB, starting from a previously prepared system and using a minimalistic QC region. We will combine reaction coordinate scans with umbrella sampling.

This video tutorial uses the classic example of the enzyme Triose Phosphate Isomerase (TIM) to cover the following aspects: how to load a system, edit/reduce the number of atoms (pruning), energy minimization, selection of a QC region, and the scan of the first step of the catalytic cycle.

In this series of tutorials, we will explore the reaction catalyzed by the enzyme chorismate mutase (CM), with a particular focus on various sampling and analysis strategies. Special thanks to Dr. Atsu Agbaglo and Professor Nathan DeYonker from the University of Memphis for their assistance with the original files and valuable suggestions.

In this tutorial, we will use relaxed potential energy surface scans to simulate the reaction catalyzed by the enzyme β-phosphoglucomutase (PGMase), which converts β-glucose-1,6-bisphosphate into β-glucose-6-phosphate.