Software

 

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.
 
Download:
The software, manual and tutorial are available from GitHub
 
Developers:

Matteo Degiacomi
Valentina Erastova

Reference:

M. T. Degiacomi, V. Erastova, M. 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) 

Download:

Software and the manual are on GitHub

Developers:

Valentina Erastova
Matteo Degiacomi

Reference:

M. T. Degiacomi, S. Tian, H. C. Greenwell, V. Erastova, DynDen: Assessing convergence of molecular dynamics simulations of interfaces, Computer Physics Communications, Volume 269, 2021

 


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