Summary & Purpose
We incorporated Espaloma forcefield parameterization into MoSDeF tools for performing molecular dynamics simulations of organic molecules with HOOMD-Blue. We compared equilibrium morphologies predicted for perylene and poly-3-hexylthiophene (P3HT) with the ESP-UA forcefield in the present work against prior work using the OPLS-UA forcefield. We found that, after resolving the chemical ambiguities in molecular topologies, ESP-UA is similar to GAFF. We observed the clustering/melting phase behavior to be similar between ESP-UA and OPLS-UA, but the base energy unit of OPLS-UA was found to better connect to experimentally measured transition temperatures. Short-range ordering measured by radial distribution functions was found to be essentially identical between the two forcefields, and the long-range ordering measured by grazing incidence X-ray scattering was qualitatively similar, with ESP-UA matching experiments better than OPLS-UA. We concluded that Espaloma offers promise in the automated screening of molecules that are from more complex chemical spaces.
Date of Publication or Submission
1-13-2024
DOI
https://doi.org/10.18122/mse_data.42.boisestate
Funding Citation
This research was funded by NSF grant number 2411302.
Single Dataset or Series?
Single Dataset
Data Format
*.gsd; *.txt
File Size
1.44 GB
Data Attributes
This dataset presents the most ordered trajectories of P3HT and perylene generated via molecular dynamics simulations.
Time Period
2023-2025
Privacy and Confidentiality Statement
Boise State is explicitly compliant with federal and state laws surrounding data privacy including the protection of personal financial information through the Gramm-Leach-Bliley Act, personal medical information through HIPAA, HITECH and other regulations. All human subject data (e.g., surveys) has been collected and managed only by personnel with adequate human subject protection certification.
Use Restrictions
Users are free to share, copy, distribute and use the dataset; to create or produce works from the dataset; to adapt, modify, transform and build upon the dataset as long as the user attributes any public use of the dataset, or works produced from the dataset, referencing the author(s) and DOI link. For any use or redistribution of the dataset, or works produced from it, the user must make clear to others the license of the dataset and keep intact any notices on the original dataset.
Disclaimer of Warranty
BOISE STATE UNIVERSITY MAKES NO REPRESENTATIONS ABOUT THE SUITABILITY OF THE INFORMATION CONTAINED IN OR PROVIDED AS PART OF THE SYSTEM FOR ANY PURPOSE. ALL SUCH INFORMATION IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND. BOISE STATE UNIVERSITY HEREBY DISCLAIMS ALL WARRANTIES AND CONDITIONS WITH REGARD TO THIS INFORMATION, INCLUDING ALL WARRANTIES AND CONDITIONS OF MERCHANTABILITY, WHETHER EXPRESS, IMPLIED OR STATUTORY, FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT.
IN NO EVENT SHALL BOISE STATE UNIVERSITY BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF INFORMATION AVAILABLE FROM THE SYSTEM.
THE INFORMATION PROVIDED BY THE SYSTEM COULD INCLUDE TECHNICAL INACCURACIES OR TYPOGRAPHICAL ERRORS. CHANGES ARE PERIODICALLY ADDED TO THE INFORMATION HEREIN. COMPANY AND/OR ITS RESPECTIVE SUPPLIERS MAY MAKE IMPROVEMENTS AND/OR CHANGES IN THE PRODUCT(S) AND/OR THE PROGRAM(S) DESCRIBED HEREIN AT ANY TIME, WITH OR WITHOUT NOTICE TO YOU.
BOISE STATE UNIVERSITY DOES NOT MAKE ANY ASSURANCES WITH REGARD TO THE ACCURACY OF THE RESULTS OR OUTPUT THAT DERIVES FROM USE OF THE SYSTEM.
Recommended Citation
Paul, Madilyn E.; Jones, Chris D.; and Jankowski, Eric. (2024). Dataset for Validating Structural Predictions of Conjugated Macromolecules in Espaloma-Enabled Reproducible Workflows [Data set]. Retrieved from https://doi.org/10.18122/mse_data.42.boisestate
