Software

figure1
A1Assemble! is 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

 


logo_den_dyn2DynDen – a tool to access convergence of MD simulations of surface phenomena

Available on GitHub (currently private repo)

Developers:
Valentina Erastova
Matteo Degiacomi

 



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