I am currently studying the basics of simulation and want to try out some experiments. It is a known fact that gold nanoparticles can bind to chemical groups which contains thiol (R–SH group). I want to simulate the binding of a thiol group to a gold nanoparticle. How can I do this? Where do I have to start? Which software can be used for this purpose?
Density Functional Theory is worth investigating if you're looking for a fairly efficient way of investigating these interactions at an electronic level. The term 'nanoparticle' is wonderfully vague as it encompasses two to three orders of size magnitude - the size of the nanoparticle will inform the specific choice of method:
Small (as in, only a couple of atoms) nanoparticles are amenable to computation with atom-centered basis sets in programs such as Gaussian, ADF, ORCA, GAMESS and so on. The latter two may be acquired free for academic use. If your particle/ligand complex is highly symmetric and/or you have supercomputer time you might be able to work with a moderately large particle. I recall a paper abstract where researchers did TDDFT on a 120 atom silver nanoparticle in ADF (here it is!), aided by high symmetry.
Large systems, where it's a) computationally unreasonable to model the whole particle and b) to a first-order approximation the ligand-particle interaction can be treated as occurring on an infinite plane or edge, may be more amenable to periodic DFT using plane-wave basis sets (PW-DFT). There are many codes available, ranging from free to very expensive. Off the top of my head, VASP, SIESTA, Quantum Espresso, Abinit and CASTEP are fairly popular.
There's also an atom-centered periodic franken-version of ADF called ADF-BAND which can model 1D to 3D periodic systems, which is worth mentioning. It is not particularly well documented, however.