tmQM-xtb dataset
DOI10.5281/zenodo.14919908Zenodo14919908MaRDI QIDQ6698048FDOQ6698048
Dataset published at Zenodo repository.
John Chodera, Shuai Yan, Christopher R. Iacovella
Publication date: 24 February 2025
Copyright license: Creative Commons Attribution 4.0 International
This provides an hdf5 file for the tmQM-xtb dataset. This dataset was generated starting from the tmQM dataset (release 13Aug2024, https://github.com/uiocompcat/tmQM) containing 108541 unique molecules; each molecule was evaluated using gfn2-xtb, and then a short MD simulation performed to provide additional configurations of the molecules. The tblite package was used to evaluate the energetic of the system using the gfn2-xtb formalism. MD simulations were performed using the Atomic Simulation Environment (ASE), using the Langevin integrator Simulations were performed at 400K with a 1 fs timestep and 0.01 1/fs friction damping factor. In all trajectories, the first configuration corresponds to the energy minimized configuration reported in the original tmQM dataset. 100 steps were taken between snapshots, with 10 total snapshots per molecule During MD sampling, gfn2-xtb accuracy was set to 2; all reported properties were calculated at accuracy level 1. Scripts used to perform the sampling can be found https://github.com/chrisiacovella/xtb_config_gen Note, this dataset correpsonds to the raw output of the gfn2-xtb based calculations. No validation or exclusions have been made and thus not all configurations will necessarily be stable or realistic. Note, this version now inclues units for each entry; these were inadvertantly left out in the prior version
This page was built for dataset: tmQM-xtb dataset
