Downloads

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