Data deposition for scientific article "Destabilization of Structured RNAs by OPC and TIP4PD Water Models"

This dataset accompanies the scientific article "Destabilization of Structured RNAs by OPC and TIP4PD Water Models." It contains all molecular dynamics trajectories reported in the manuscript, along with the scripts and input files required to reproduce the calculations. Due to Zenodo’s strict data-size limits, the deposited trajectory files are strided by a significant factor of at least 100 relative to the original data on which the analyses were performed. This could lead to confusion as the number of frames no longer corresponds to any specific simulation length. For the exact simulation lengths, please refer to Table 1 in the main text. With the exception of the mixed water box simulations, all the trajectories are provided without water molecules. For all scientific or technical inquiries regarding this dataset, please contact the corresponding author, Dr. Miroslav Krepl. ***IMPORTANT NOTE***. Due to technical issues, we were unable to upload some of the datasets to Zenodo. These issues occurred during the Christmas 2025 break, and we were unable to resolve them with Zenodo staff prior to the revision deadline (January 3, 2026). As a temporary solution, the two missing datasets are available at the following address: https://owncloud.cesnet.cz/index.php/s/63qMW1vINF3Q4fk Once these datasets can be uploaded to this Zenodo archive, an update notice will be posted.