I have a very general question but still quite important since I didn't find convincing tools to get the structural analysis done for LAMMPS dump file (trajectories). I am looking for post processing tools to understand:
(i) Number (and lengths?) of hydrogen bonds between sets of molecules/atom-indices as a function of time. Also, does the tool take into account periodicity for hydrogen bond formers across the the unit cell?
(ii) Find distances between sets of molecules/atom-indices as a function of time including effect of periodicity.
(iii) Thoughts on other (except RDF, which is calculated pretty reliably from several softwares like VMD etc) interesting structural features that could be analyzed from the trajectories are welcome too.
Please include helpful resources/links on tutorials of those softwares if you can.