We present here a VMD builder for carbon dots (CD) and a full protocol for their further molecular dynamics (MD) simulations.
Our CD builder was developed in order to easily build a model of carbon dots that may contain several oxygen containing groups on the surface (see Downloads) and we provide here several sample structures ready for MD simulations.
Our modification can be easily added to already installed VMD by simply copying several tcl scripts (see Manual/Tutorial).
We will continue in developing in this field by parameterizing other surface groups and doping of CD interior. You can contact us with your questions, issues or ideas for development.