Tutorials

Tutorials to help you get familiar with KIMMDY.

Get Started

user

In this tutorial we will be simulating hydrogen atom transfer in a simple ACE/NME-capped Alanine molecule in a box of water.

Modify a Topology

user

In this tutorial we will check out different ways to process GROMACS topology files with the command-line interface kimmdy-modify-top. Use kimmdy-modify-top -h to see the…

Run KIMMDY from Colbuilder fibril

user

In this tutorial we will download a collagen fibril from colbuilder and run a KIMMDY simulation on it.

Write a Reaction Plugin

developer

In this tutorial, you will learn how to create your own reaction plugin in a GitHub repository.