Erastova Group

School of Chemistry, University of Edinburgh

Erastova Group GitHub Resources

Welcome to the GitHub page of the Erastova Group. We build and share codes, molecular models, teaching materials, and working resources for molecular modelling of natural minerals and materials.

Visit erastova.xyz

Codes

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.

Biochar Development

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 covering the set-up and use of biochar molecular models, described in the works above.

ClayCode

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 Materials

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.