Overview

Molecular Dynamics Simulations of Small Molecules

Skill Level: Intermediate 

Language: English

Workload: 2 hours total

Topic: Computational chemistry

Overview: 

Lecture 1 – Molecular Dynamics simulation of butane and analysis of torsion angle

Lecture 2 – Molecular Dynamics simulation of pentane and calculation potential of mean force

Lecture 3 – Molecular Dynamics simulations of multiple ethane molecules in water box and calculation of diffusion coefficient

Course Description: Molecular dynamics (MD) simulations of small molecules, such as ethane, butane, and pentane, are performed in an applied manner. The MD simulations are executed using NAMD, and the visualization of the simulations is done with VMD. The analyses of features and material properties of molecules are calculated using the Python programming language.

Course Contents:

Lecture 1 – Molecular Dynamics simulation of butane and analysis of torsion angle

Lecture 2 – Molecular Dynamics simulation of pentane and calculation potential of mean force

Lecture 3 – Molecular Dynamics simulations of multiple ethane molecules in water box and calculation of diffusion coefficient

Who Should Enroll: Anyone who wishes to learn running and analyzing an MD simulation.

Prerequisite(s):

Basics of Molecular Dynamics simulation and its analyses

An in-depth information of force-fields

Computing energy surface of a small molecule

Bonded and non-bonded interactions that govern dynamics

Tools, libraries, frameworks used: Python, VAMD, NAMD2

Learning Objectives:

Basics of Molecular Dynamics simulation and its analyses

An in-depth information of force-fields

Computing energy surface of a small molecule

Bonded and non-bonded interactions that govern dynamics 

About the instructor(s): https://midst.sabanciuniv.edu/people.html