AutoMeKin

Introduction

AutoMeKin (formerly known as tsscds) is a computer program that has been designed to discover reaction mechanisms and solve the kinetics in an automated fashion. AutoMeKin finds transition state structures connecting intermediates and product fragments using MD simulations and Graph Theory algorithms. Then, Kinetic Monte Carlo simulations give additional information, i.e., kinetic results at the selected conditions. The user only needs to provide a starting structure of the system. So far, the electronic structure programs MOPAC2016 and Gaussian 09 (G09) are interfaced with AutoMeKin.

Details of the method are described in these two publications: 1 2

Users are encouraged to read the tutorial, which is thought to guide you through the various steps necessary to predict reaction mechanisms and kinetics of unimolecular decompositions. To facilitate the presentation, we consider, as an example, the decomposition of formic acid (FA).

The program has been tested on the following Linux distros: CentOS 7, Red Hat Enterprise Linux and Ubuntu 16.04.3 LTS

To give you a flavor of the capabilities of the program you can try our web interface

Authors

George L. Barnes, Sabine Kopec, Emilio Martinez-Nunez, Daniel Pelaez-Ruiz, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, James J. P. Stewart, Pablo G. Tahoces and Saulo A. Vazquez

Address
Departamento de Química Física, Facultade de Química, Avda. das Ciencias s/n, 15782 Santiago de Compostela, SPAIN
email me

License

MIT License

Copyright (C) 2018 George L. Barnes, Sabine Kopec, Emilio Martinez-Nunez, Daniel Pelaez-Ruiz, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, James J. P. Stewart, Pablo G. Tahoces and Saulo A. Vazquez

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

Downloads

Download the tutorial
The most recent version of AutoMeKin can be downloaded here
A stable (but maybe not up-to-date) version can also be cloned from:
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Install the code

To install the code read the Installation instructions

Program execution

To start using any of the scripts of the program, load the amk/2018 module:

module load amk/2018

To run the low-level calculations use:

nohup llcalcs.sh molecule.dat ntasks niter runningtasks >llcalcs.log 2>&1 &

where:
molecule is the name of your molecule
ntasks is the number of tasks
niter is the number of iterations
runningtasks is the number of simultaneous tasks

To run the high-level calculations use:

nohup hlcalcs.sh molecule.dat runningtasks >hlcalcs.log 2>&1 &

For more details, follow the instructions given in the tutorial

References and citations

These four publications must be cited in any work presenting results obtained with our software:

1. E. Martínez-Núñez J. Comput. Chem. 2015, 36, 222
2. E. Martínez-Núñez Phys. Chem. Chem. Phys. 2015,17, 14912
3. A. Rodriguez, R. Rodriguez-Fernandez, S.A. Vazquez, G.L. Barnes, J.J.P. Stewart, E Martínez-Nuñez, J. Comput. Chem. 2018, 39, 1922
4. J. J. P. Stewart, MOPAC2016, Stewart Computational Chemistry: Colorado Springs, CO, USA, HTTP://OpenMOPAC.net, 2016.

Publications using AutoMeKin:

5. A. Esteban et al. Tetrahedron (2019), doi: https://doi.org/10.1016/j.tet.2019.130764
6. R. A. Jara-Toro et al. ChemSystemsChem doi: 10.1002/syst.201900024
7. R. Panades-Barrueta et al. Frontiers in Chemistry 2019, 7, 576
8. S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008
9. V. Macaluso et al. J. Phys. Chem. A 2019, 123, 3685-3696
10. S. A. Vázquez et al. Molecules 2018, 23, 3156
11. A. Rodríguez et al. J. Comput. Chem. 2018, 39, 1922-1930
12. D. Ferro-Costas et al. J. Phys. Chem. A 2018, 122, 4790-4800
13. Y. Fenard et al. Combust. Flame. 2018, 191, 252-269
14. M. J. Wilhelm et al. ApJ. 2017, 849, 15
15. J. A. Varela et al. Chem. Sci 2017, 8, 3843-3851
16. E. Rossich-Molina et al. Phys. Chem. Chem. Phys. 2016, 18, 22712-22718
17. R. Pérez-Soto et al. Phys. Chem. Chem. Phys. 2016, 18, 5019-5026
18. S. A. Vázquez and E. Martínez-Núñez, Phys. Chem. Chem. Phys. 2015, 17, 6948-6955

Changelog

Consult the Latest changes

Web interface

AutoMeKin can be used through our web interface.

News

The improvements briefly described below will be available in AutoMeKin2020.

AutoMeKin has been interfaced with BXDE to enhance its efficiency: R. A. Jara-Toro et al. ChemSystemsChem doi: 10.1002/syst.201900024

The method has also been recently generalized in a collaboration with Dani Pelaez and co-workers to study van der Waals structures ( S. Kopec et al. Int. J. Quantum Chem. 2019, 119, e26008 ) and also to generate sum-of-products PESs for quantum dynamics.

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