programing-tutorial

This tutorial covers the concept of python programming in three types:

1. Flat Python script

2. Python program with functions

3. Object-oriented Python project with classes

We will implement a molecular dynamics (MD) program using each of the above three type and discuss the best practices.

MD Simulation Program Outline

1. Create a molecular system.

2. Setup force field.

3. Run simulation by integrating the equation of motion.

4. Analyze trajectory.

Requirements

• Python 3.6
• Numpy
• pytest
• setuptools

Folder structure

Three top folders corresponds to the three types of python programs.

In each top folder, there will be a README.md for some notes.

The rest of the files and folders in each top folder shows an example structure of the type.

Topics

• version control (git)

• conda env