Assemble! 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
DynDen – 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