Data for the paper titled "Unravelling 2,4-D – biochar interactions by molecular dynamics: adsorption modes and surface functionalities" by Rosie Wood, Ondřej Mašek, and Valentina Erastova. Biomass and Bioenergy 210 (2026): 109080 10.1016/j.biombioe.2026.109080.
The data is organised as follows:
- Each directory contains data for a specific biochar --
BC400,BC600, andBC800. - The sub-directories withing biochar directory correspond to given concentrations --
c1,c2, ...c8. - Within these subdirectories the following files are given:
eq_sys.gro-- equilibrated biochar + 2,4-D + water system;system.topol-- topology file for the given system;mdout.mdpandtopol.tpr-- compiled files for production run.
- We also provide:
- include topology files (
.itp) and atom type files (.atp) for biochars within biochar directory and for 2,4-D within main directory; gra_oplsaa.ff-- an OPLS-AA folder within main directory.- These files are linked within the
system.topof all systems.
- include topology files (
The details on constructing and validating biochar models used in this work can be found in:
- Rosie Wood, Ondřej Mašek, and Valentina Erastova. "Developing realistic molecular models of biochars." Cell Reports Physical Science 5.7 (2024). doi.org/10.1016/j.xcrp.2024.102037; and
- downloaded from github.com/Erastova-group/Biochar_MolecularModels.
Any questions, please open an issue or email valentina.erastova@ed.ac.uk
If you use our models please cite our work:
- Rosie Wood, Ondřej Mašek, and Valentina Erastova. "Unravelling 2,4-D – biochar interactions by molecular dynamics: adsorption modes and surface functionalities." Biomass and Bioenergy 210 (2026): 109080 10.1016/j.biombioe.2026.109080.
- Valentina Erastova. "Erastova-group/24D_biochar: zenodo (v1.1)" Zenodo. doi.org/10.5281/zenodo.17990328 (2025).
- Rosie Wood, Ondřej Mašek, and Valentina Erastova. "Developing realistic molecular models of biochars." Cell Reports Physical Science 5.7 (2024).