Software

We distribute our software and datasets via GitHub.com/Erastova-Group

Check erastova-group.github.io for more information about our projects

ClayCode

ClayCode generates clay mineral structures based upon their natural partially ocupied unit cell compositions and assigns ClayFF forecefield parameters, generating all the input files ready for simulation with Gromacs software.

MANUAL:

The software, manual and tutorial are available from erastova-group.github.io/ClayCode

Reference:

Hannah Pollak, Matteo T. Degiacomi, and Valentina Erastova. Modelling realistic clay systems with ClayCode. Journal of Chemical Theory and Computation, 2024: in press. DOI: 10.1021/acs.jctc.4c00987

Assemble!

a program greatly simplifying the preparation of molecular dynamics simulations of polymeric systems. It allows the creation of the desired system of polymer chains from constituent monomers, packs the chains into a box according to the required concentration and returns all the files needed for simulation with GROMACS. Assemble! is developed in Python, and can be controlled both via terminal and a graphical user interface.

Download:

The software, manual and tutorial are available from GitHub

Reference:

Matteo T. Degiacomi, Valentina Erastova,and Mark R. Wilson, Easy setup of molecular dynamics simulations of polymeric mixtures with Assemble!, Computer Physics Communications, Volume 202, 2016

DynDen

a tool to access convergence of MD simulations of surface phenomena (and to print dinosaurs)

Download:

Software and the manual are on GitHub

Reference:

Graphene Oxide Builder

A useful visual tool to build graphene oxide, with edges/holes, -C=O, -COOH, -O- and -OH on demand.

First developed by Wu Tongfei

The updated version, with small fixes and functionality, can be downloaded from GitHub