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Molecular Dynamics Simulations

Molecular dynamics

Prerequisites and installations

Module: Installation of necessary software
Installation of tools: WSL2/Linux etc.

Linux basics

Linux - the basics
Linux: Some basic & useful commands

Python and Jupyter

Summary
Jupyter Notebook / Jupyter Lab
Brief introduction to Python

Molecular interactions

Interactions

Numerical algorithms

Digression: A few words about finite precision
Basic MD algorithm
Integration of the equations of motion

Review of thermodynamics and statistical mechanics

Review of thermodynamics

Visualization

Molecular visualization
VMD molecular visualization software
VMD selections
VMD plugins

MD basics

First look into (particle) simulations
What is Molecular Dynamics (MD)
Boundary conditions (BCs)

MD simulation with Gromacs

Introduction to Gromacs
Gromacs installation
Simple simulation of water using Gromacs

Installation instructions

Installation of Python and Jupyter
Python virtual environments
VMD installation

Extras & How-Tos

On computation and codes
Editing ASCII files
The vi editor
Helpful software

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repository
open issue

Index

By Mikko Karttunen
© Copyright 2022.