Published April 6, 2020 | Version v1
Dataset Open

Data-Driven Collective Variables for Enhanced Sampling

  • 1. Department of Physics, ETH Zurich, 8092 Zurich, Switzerland and Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera italiana, 6900 Lugano, Switzerland
  • 2. Department of Chemistry and Applied Biosciences, ETH Zurich, 8092 Zurich, Switzerland and Facoltà di Informatica, Instituto di Scienze Computazionali, Università della Svizzera italiana (USI), 6900 Lugano, Switzerland

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Description

Designing an appropriate set of collective variables is crucial to the success of several enhanced sampling methods. Here we focus on how to obtain such variables from information limited to the metastable states. We characterize these states by a large set of descriptors and employ neural networks to compress this information in a lower-dimensional space, using Fisher's linear discriminant as an objective function to maximize the discriminative power of the network. We test this method on alanine dipeptide, using the non-linearly separable dataset composed by atomic distances. We then study an intermolecular aldol reaction characterized by a concerted mechanism. The resulting variables are able to promote sampling by drawing non-linear paths in the physical space connecting the fluctuations between metastable basins. Lastly, we interpret the behavior of the neural network by studying its relation to the physical variables. Through the identification of its most relevant features, we are able to gain chemical insight into the process.

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References

Journal reference (Paper in which the method is described)
L. Bonati, V. Rizzi, M. Parrinello, J. Phys. Chem. Lett., 11, 2998-3004 (2020), doi: 10.1021/acs.jpclett.0c00535

Software (The latest release of the code)
Github repository

Software (Tutorial for the training of the Deep-LDA CV)
Google Colab notebook

Preprint (Open-access preprint of the method)
L. Bonati, V. Rizzi, M. Parrinello, arXiv:2002.06562