[gmx-users] metal nanoparticles

Nima Sa nimavaeesa at yahoo.com
Fri Jul 3 23:02:46 CEST 2015

Thank you Alex for the comprehensive reply.

     On Saturday, July 4, 2015 1:12 AM, Alex <nedomacho at gmail.com> wrote:

 People do this all the time, e.g. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114152
Unfortunately, the models and the resulting data are worth very
little, because the simulated nanoparticles arent't made of metal.
They are blobs of van der Waals particles, instead.

The explanation would be beyond a board post. In short, if I absolutely had to simulate this stuff with MD, I
would use ReaxFF forcefield under LAMMPS, although it also doesn't have the
concept of dynamic polarizability, Fermi gas, etc, etc. Further, and
this is critically important, many things would depend on the size of
your nanoparticle, as its "metallicity" is a function of size. One can
have semiconducting or even dielectric nanoparticles made out of
materials, which are metallic in bulk.

The "proper" way is to use DFTMD, which will require massive computational power.
Metals are the worst materials to simulate using  the biomolecular
style forcefields. On the other hand, however, people do this, adding
to the infinite bath of worthless results. It passes peer review, and
that's all that matters, right? :)


NS> Hi,Dear users and JustinI want to perform MD simulations on gold
NS> nanoparticles and have a couple of questions to ask. For example I
NS> want to equilibrate a gold nanoparticle in a box of solvent. As I
NS> went through the existing data on the Internet I found nothing on
NS> this issue. Now, Is Gromacs capable of doing this? Which force
NS> field should I use for the metal nanoparticles? If Gromacs is
NS> unable to do this, Is there another software that can do this? It
NS> seems that OpenMD can do this (Please see Building and
NS> equilibrating a gold nanoparticle in OpenMD « OpenMD. Is it OK to
NS> use this code for this purpopse?Thank you very much.


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