Get Started

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Author

Jannik Buhr

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

Installation

Prerequisites

  • python3.9 or higher
  • gromacs (tested with version 2021.4, gmx should be available in the PATH)

Optional:

  • plumed-patched version of gromacs (for the homolysis reaction).

Let’s first create a directory and a virtual environment for kimmdy:

mkdir kimmdy-tutorial
cd kimmdy-tutorial
python -m venv .venv
source .venv/bin/activate

To install KIMMDY, the builtin reaction plugins and the analysis tools use

pip install kimmdy[reactions,analysis]

Setup the Simulation

Download and unzip the input files to this directory.

# TODO: add link to gihtub user content
wget ...
unzip setup.zip

The kimmdy.yml file should look like this:

kimmdy.yml
dryrun: false
max_tasks: 100
name: 'hat_tf_000'
gromacs_alias: 'gmx'
top: 'Ala_out.top'
gro: 'npt.gro'
ndx: 'index.ndx'
mds:
  equilibrium:
    mdp: 'md.mdp'
  relax:
    mdp: 'md_slow.mdp'
changer:
  coordinates:
    md: 'relax'      
reactions:
  hat_reaction:
    frequency_factor: 100000000
    h_cutoff: 3
    polling_rate: 1

sequence:
- equilibrium
- mult: 2
  tasks:
  - equilibrium
  - reactions

Our starting structure is a simple ACE/NME-capped Alanine molecule in a box of water. Note, how it has a missing hydrogen atom on the alpha carbon. This is a radical. We will use the builtin hat_reaction to simulate hydrogen atom transfer reactions from nearby hydrogens to the radical position.

Start the KIMMDY run with the kimmdy command:

Run the Simulation

kimmdy

You can also run kimmdy directly from python with

from kimmdy.cmd import kimmdy_run
kimmdy_run()

Analyse the Simulation

Concatenate the trajectories from the individual steps into one for viewing:

kimmdy-analysis trjcat alanine_hat_000 --open-vmd

Check the energy of the system:

kimmdy-analysis energy alanine_hat_000 --open-plot --terms Potential Kinetic

Energy plot

Visualize where the radicals end up:

kimmdy-analysis radical_population alanine_hat_000 --open-plot --open-vmd

In VMD, color the atoms by beta factor to show the radical occupancy.

VMD representation settings

Radical population plot

Plot the reaction rates:

kimmdy-analysis rates alanine_hat_000

In the alanine_hat_000/analysis directory you will then find a plot of rates for each possible reaction at every step they were queried, e.g.

Reaction rates plot

Or do all of the above directly from python:

from kimmdy.analysis import concat_trj, plot_energy, radical_population, plot_rates
concat_trj('alanine_hat_000', open_vmd=True)
plot_energy('alanine_hat_000', terms=['Potential', 'Kinetic'], open_plot=True)
radical_population('alanine_hat_000', open_plot=True, open_vmd=True)
plot_rates('alanine_hat_000')

Congratulations, you have successfully run your first KIMMDY simulation!

Next steps

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