Hello. I am quite new to MD so apologies in advance for taking your time and thanks!
I created a soot particle (containing >800 C and couple of H) with ReaxFF and now I would like to see the absorption of water molecules on this particle using Lennard Jones potentials. How can I create a field to capture the interactions of water molecules and all surface C atoms on the particle? Do I need to define all angles, dihedrals, impropers and so on for each atom or is there another way to do that? Because I would like to freeze the particle and only see the behavior of water molecules on the different sites of the particles. Thanks a lot!
In that case you can simply exclude the carbon atoms from any fix updated the atom positions. In that case, no need to define intra-molecular parameters for the soot structure. The only parameters that you will need to define are the cross LJ interactions between carbon and water.
Thank you! The C atoms on the surface of the particle have different hybridizations. Will I be able to capture the effect of that on the water absorption with this method?
You will have to check the background literature on that – this site is run by volunteers who are generally experienced with LAMMPS but not necessarily with specific chemical research areas, and even after you did get an answer from someone you would have to validate it with a literature citation.
As a tip – locate the paper you are citing for your parameters (you do have to cite those too!). Then look on Google Scholar for papers that have cited that paper. If your parameters are suitable for your application you will find other papers that have done similar things (you may even have been beaten to publication!). If, on the other hand, you don’t, that may signal to you that the parameters you are using may be less suitable.
Finally, remember that classical MD is not particularly suitable for studying chemical reactions especially compared to DFT (or emerging machine learning force fields trained on DFT). User beware!
Hello. Well suprisingly, I know how to do research. My question is not related to the novel approach to the problem, instead it was related to the software/simulation approach. Being new to the area can arise many questions including very simple ones. That is why I believe this forum is created so that the volunteers/experts can help by saying even one two very basic sentences and helping beginners a lot to make sense some things. For example the previous reply was very helpful to me and I already managed to make a progress. It is actually very interesting that there are always irrelevant responses in many questions, mostly diminishing people’s efforts and so on. I hope that this forum will still encourage people to “ask” for the sake of knowledge and progress.
you might find some relevant reaxff articles at:
https://alphataubio.com/fitsnap/reaxff.html#reaxff-bibliography