I hope you feel great.
I have two questions:
1- I pyrolysis a box consisting of 10 chains of polymer, and for this purpose, I used the Reax-FF. After pyrolysis, I want to know which molecules and how many of them are produced. Could you please suggest tools for post-processing after pyrolysis?
This is actually best done during the simulation by also running a command like fix reaxff/species and/or fix reaxff/bonds. This analyses the bonding structure using the internal ReaxFF data and thus is the most reliable. Of course you can also use heuristic bond analysis with a distance based bond search. VMD for example has a such a feature that can be used via VMD/Tcl scripting; however, for that to work, you need to assign suitable covalent radii and assign elements for the internal VMD data to be able to correctly post-process the trajectory data.
2- The other question is about investigating gas adsorption on the final structure after pyrolysis. I ran all simulations for pyrolysis in the NVT ensemble. For studying adsorption, do I need to bring the final structure to atmospheric pressure with the NPT ensemble?
Unless you need a significantly elevated pressure, there is no need to bother. At the length scale of your simulation, there is are other factors causing much larger systematic errors than the difference between vacuum and 1 atm pressure. So if you left sufficient space for the first part of your simulation, you don’t need to worry about NPT for the second (and thus save yourself a lot of headaches).
Read more here: Source link