Installation
Find your VMD plugins folder ($VMD/plugins/noarch/tcl) and replace nanotube1.5 with the provided nanotube1.5 folder (carbondot.tcl, gui.tcl and pkgIndex.tcl are the required files, graphene.tcl and nanotube.tcl are not modified from the original version).
The default nanotube1.5/ folder includes gui.tcl that can be replaced by a provided gui_tooltip.tcl (but keep the name gui.tcl). This can be done only on the VMD versions including tooltip package. The gui_tooltip.tcl includes help messages reacting on the mouse position in the gui window.
Carbon dot building
Open VMD and menu Extensions – Modeling – Nanotube Builder
Choose your options and Generate the dot. If you want your structure and topology file to be saved, choose a path, where to save them. The files with automated names (e.g. dot_0.5_hydroxyl.pdb, dot_0.5_hydroxyl.top) will be saved by clicking on ‘Generate Dot’ if the path is provided.
If you want to adjust the dot (e.g. add different functional groups at desired places), use the last part of the tools and click on the button with the group. You will be switched into the picking mode and click on the hydrogen atom you want to replace by this group. You can do this multiple times. Be aware that if you click on different place than you wanted, an error structure will appear!
If you want to delete a group, delete its atoms one by one. The deleted atoms will stay in the structure as ‘QQ’ and you can remove them easily afterwards.
Simulations
If you want to run the simulations, you need to adjust the topology files (charges, order of atoms etc.). Move to Unix environment and into provided folder ‘Builder’, move your .pdb and .top files there as well.
For the final part of the process, you need to have Gromacs 5.x installed! If you have lower versions, you need to adjust the commands (gmx …) and .mdp files accordingly.
If your files are called dot.pdb and dot.top, type:
./Dot_sort.sh dot.pdb dot.top
(adjust the file names in the command in case you have different). The script will assign the charges, create molecule_*.itp and molecule*.pdb files (for individual layers), minimize the dot, solvate and ionize it, minimize it again and then perform a short (1 ns) equilibration simulation. Mdp files run in Gromacs 5.x version.