Monday, April 29, 2019

Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical Calculations

Highlighted by Jan Jensen


The paper describes a new way to search for conformers, chemical reactions, and estimate barriers using the semiempirical GFNn-XTB method using meta-dynamics. A force term is included that scales exponentially with the Cartesian RMSD from previously found structures, thereby forcing the MD explore new areas of phase space. For simulations with more than one molecule it is necessary to add a constraining potential so that the RMSD cannot be increased simply by increasing the distance between molecules. Each individual MD can be relatively short and most of the CPU time is actually spend on energy minimising the snapshots that are saved.

The results depend on a few hyperparameters, so several MD simulations with different values are run in parallel. Because of the extra force the temperature is also a hyperparameters so the method doesn't necessarily tell you what reactions are most likely to occur at, say, 300K.

The conformational search is tested on 22 (mostly) organic molecules and includes the GFN2-xTB energies of the lowest energy conformer for each molecules. This is a valuable benchmark set for other conformational search algorithms designed to find the global minimum.


This work is licensed under a Creative Commons Attribution 4.0 International License.

1 comment:

  1. The results depend on a few hyperparameters, so several MD simulations with different values are run in parallel. Because of the extra force the temperature is also a hyperparameters so the method doesn't necessarily tell you what reactions are most likely to occur at, say, 300K. EADA105 dumps

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