KIMMDY
Getting Started
How-To
Tutorials
Explanations
Reference
Source Code
Report a Bug
Tutorials
KIMMDY
Tutorials
Run KIMMDY from Colbuilder fibril
Get Started
Modify a Topology
Write a Reaction Plugin
How-To
Analyze a KIMMDY run
Contribute
Examples
High Performance Computing
Install Machine Learning Plugins
Reaction only
Explanation
Components of KIMMDY
Visualize Topologies
Reference
Input File
CLI Arguments
Python API
cmd
Topology
topology.topology
topology.ff
topology.utils
topology.atomic
parsing.TopologyDict
Reaction Plugins
homolysis.reaction.Homolysis
hat_naive.reaction.NaiveHAT
dummyreaction.reaction.DummyReaction
Other Modules
constants
coordinates
config
kmc
parsing
runmanager
tasks
recipe
plugins
analysis
utils
tools
Categories
All
(4)
developer
(1)
user
(3)
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.
Jannik Buhr
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…
Eric Hartmann
Run KIMMDY from Colbuilder fibril
user
In this tutorial we will download a collagen fibril from colbuilder and run a KIMMDY simulation on it.
Eric Hartmann
Write a Reaction Plugin
developer
In this tutorial, you will learn how to create your own reaction plugin in a GitHub repository.
Eric Hartmann
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KIMMDY
Run KIMMDY from Colbuilder fibril
