ClayCode
MANUAL:
Assemble!
Download:
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 (and to print dinosaurs)
Download:
Software and the manual are on GitHub
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