Welcome to the GitHub page of the Erastova Group.

We are a research group at the School of Chemistry, University of Edinburgh, interested in molecular models of natural minerals and materials. This page brings together our codes, molecular models, teaching materials, and working resources.

To learn more about the group, visit: erastova.xyz

Software and scripts developed by the group to support molecular simulation setup, analysis, and interpretation.

• DynDen
  A software to assess convergence of molecular dynamics simulations of interfacial phenomena.

• Assemble!
  A tool for generating atomistic polymeric mixtures ready for simulation in GROMACS.

• ClayCode
  A tool to automate the setup of atomistic clay models for classical molecular dynamics simulations with GROMACS.

Repositories supporting the development of molecular models for biochars and their interactions with environmental species.

• Biochar_MolecularModels
  Molecular models of woody biochars at HTT 400 °C, 600 °C, and 800 °C, together with experimental property datasets.

• Porous_Biochars_Models
  Porous biochar molecular models created with the virtual atom approach, representative of woody biochars produced at 600–650 °C.

• Mn_Biochar
  Atomistic models and GROMACS files for Mn(II) interactions with wood- and straw-derived biochars.

• 24D_biochar
  Molecular dynamics study of 2,4-D adsorption on biochar.

• Tutorials
  Two tutorials coverung the set-up and use of biochar molecular models, described in the works above.

ClayCode is a stand-alone code developed to support the construction of atomistic clay models for molecular dynamics simulations.

• ClayCode
  Main ClayCode repository.

• ClayCode Workshop
  Workshop materials and tutorials for using ClayCode.

Teaching repositories and materials developed by the group. Some of these resources are hosted through Edinburgh Chemistry Teaching repositories.

• MD Research Techniques
  Materials for the “Introduction to Computational Chemistry Techniques” course at the University of Edinburgh.

• Data-Driven Chemistry
  An introductory Python course for undergraduate chemistry students.

• ClayCode Workshop
  Workshop materials for learning how to use ClayCode.

• Biochar Molecular Models Tutorials
  Guides through set-up of biochar molecular models against experimental data and simulation of adsorption using biochar molecular models.

More teaching materials will be added as they become available.

• Erastova Group website
• Erastova Group GitHub organisation
• School of Chemistry, University of Edinburgh