Package 24th January 2018
Unzip Package.zip and two folders appear. See manual for further instructions.
- VMD builder
- Building of carbon dot of any size
- Randomize addition of functional oxygen-containing groups on surface
- Manual addition of functional groups – possibility of mixed dot creation
- Deleting unwanted atoms, replacing with hydrogens
- Creating dummy topology for GROMACS, saving pdb files
- Simulation preparation
- Assignment of partial charges to atoms
- Assignment of atomic types for OPLS or AMBER99SB force field
- Hydration of the dot
Download structures:
Final structures as presented in the paper and further full simulation packages for CDs with gyration diameter of 2.1 nm after 1 μs of simulation (in OPLS) and 200 ns (AMBER99SB):
With hydrogen on edges:
| Pure CD: | Final structure | Simulation package | Simulation package |
With 30% edge coverage with functional groups:
| Func. group | Structure | OPLS | AMBER99SB |
| Hydroxyl: | Final structure | Simulation Package | Simulation package |
| Carbonyl: | Final structure | Simulation package | Simulation package |
| Carboxyl (-1): | Final structure | Simulation package | Simulation package |
| Carboxyl (0): | Final structure | Simulation package | Simulation package |
Simulations can be run from the packages by commands:
gmx grompp -f md.mdp -c *.pdb -p md.top -n
gmx_mpi mdrun