senppoa / automekin

Automated discovery of reaction Mechanisms and Kinetics

Automated Mechanisms and Kinetics (AutoMeKin)

This is the official repository of the automated reaction discovery program AutoMeKin¹.

AutoMeKin (formerly tsscds) has been designed to discover reaction mechanisms in an automated fashion. Transition states are located using MD simulations and Graph Theory algorithms. Monte Carlo simulations afford kinetic results. The only input is a starting structure in XYZ format. The method is described in these two publications: 1 2. At present MOPAC2016, Entos Qcore and Gaussian (G09/G16) are interfaced with AutoMeKin. The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 20.04 LTS.

Content

• Installation and documentation
• Developers
• Simple examples in Colab
• Web for submitting simple examples

Installation and documentation

The installation instructions and much more are detailed here

Developers

Emilio Martínez-Núñez (Universidade de Santiago de Compostela, Spain)

George L. Barnes (Siena College, USA)

Carles Bo (ICIQ, Spain)

Diego Garay-Ruiz (ICIQ, Spain)

David R. Glowacki (University of Bristol, UK)

Sabine Kopec (Université Paris-Saclay, Orsay, France)

Daniel Pelaez-Ruiz (Université Paris-Saclay, Orsay, France)

Aurelio Rodriguez (CESGA, Spain)

Roberto Rodriguez-Fernandez (Universidade de Santiago de Compostela, Spain)

Robin J. Shannon (University of Bristol, UK)

James J. P. Stewart (Stewart Computational Chemistry, USA)

Pablo G. Tahoces (Universidade de Santiago de Compostela, Spain)

Saulo A. Vazquez (Universidade de Santiago de Compostela, Spain)

Simple example in Colab

You can have a look at this Notebook to install it, test a simple example and more...

This second Notebook can be used to try some further tests.

Web site for submitting simple examples

You can also test our web site, where you can submit a simple example.

Footnotes

1. For enquiries please contact: [email protected] ↩