Software

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

ClayCode

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

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!

A1

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.

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 
logo_den_dyn2

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

Reference:

Matteo T. Degiacomi, Shansi Tian, H. Chris Greenwell, Valentina. Erastova, DynDen: Assessing convergence of molecular dynamics simulations of interfaces, Computer Physics Communications, Volume 269, 2021