Assessment of Density Functional Methods for Geometry Optimization of Bimolecular Complexes

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Overview

The purpose of this repository is to make accessible the raw data associated with the publication citation for the interested reader, to supplement the published manuscript and supplementary information (SI). To this end, we provide a self-contained environment within which to view, manipulate, and interact with these raw and post-processed data in a highly interactive format based on the Jupyter Notebook integrated development environment, in order to increase the visibility and reproducibility of the work.

Additionally, we provide discussion and executable code addressing the point-set registration problem, implementing Algorithms 1 and 2 from the SI, to illustrate the methods used in this work to assess the quality of optimized geometries.

Getting Started

To run all of the included Jupyter notebooks using the cloud-based, Jupyter Hub--hosted binder image, simply click on the pink badge above which reads "launch binder". A new tab will open containing a file browser, from which each of the included notebooks can be launched and run over an Internet connection.

NOTE: Launching the binder image the first time may take up to five minutes, as several packages must be collected, linked, and installed in the image before launch.

Repository Organization

This repository contains Jupyter notebooks and compressed, binary data files. For the raw data in CSV format, please refer to the publication's Supplementary Information. Provided here are:

1. Jupyter notebooks for data analysis and visualization
   • analysis.ipynb: Generates all relevant figures and tables from the manuscript and supplementary information
2. align.ipynb: Discusses the point-set registration problem, as well as provides implementations of Algorithms 1 & 2 from the SI
3. Data Files
   • pickles/A21_LRMSD-dCOM.pkl: Contains all LRMSD and dCOM data and summary statistics for optimizations of A21 complexes
   • pickles/HBC6-NBC7x_pes-scans.pkl: Contains raw interaction energy scans for HBC6 and NBC7x complexes
   • pickles/HBC6-NBC7x_pes-minima.pkl: Contains interpolated minima of and summary statistics for interaction energy scans of HBC6 and NBC7x complexes
   • example-geoms/: Contains example XYZ files on which the code in align.ipynb can be tested.

Citing this Repository

All future work using the code, data, and/or tools contained herein should cite the following:

1. D. A. Sirianni, A. Alenaizan, D. L. Cheney, and C. D. Sherrill. J. Chem. Theory Comput. In press, (2018)