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.

This tutorial demonstrates the use of the NEB method to investigate the interconversion between the chair and twist-boat conformations of cyclohexane. The OPLS force field is used to describe the potential energy. This approach enables the identification of the minimum energy path and estimation of the conformational barrier.

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.

This is a basic tutorial demonstrating how to load a molecular mechanics (MM) system associated with the OPLS force field and assign a small quantum chemistry (QC) region to it.

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.

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.