Hi All,
I’m trying to run an MD simulation of epoxy crosslinking using Avogadro to produce the monomers of the resin and the hardener. My approach in the MD is to create bonds whenever reactive groups come within a particular cutoff radius of each other, but this requires being able to distinguish between the reactive terminal carbons and the rest of the carbons in my epoxy. Therefore, I’d like to be able to change the ID of the terminal carbons in my Avogadro structure such that, when I convert it to an MD data file, they are considered a separate type of atom but assigned all the same characteristics.
Thus far I’ve tried messing around with their IDs in the Atom Properties menu, but all I’ve managed to do is ruin the characteristics of the whole molecule. Any help with this matter would be appreciated!