8
$\begingroup$

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.

$\endgroup$
9
$\begingroup$

There are three main Python tools that I am aware of that can do what you want and much more (and in all fairness, since you have access to all coordinates, you can code up literally whatever you want with any of these). Disclaimer: I haven't worked extensively with all of these, so make sure you try all of them, since I am not listing them in any particular order:

  1. MDAnalysis (https://www.mdanalysis.org/): good for massive trajectories, has a lot of analysis tools, but has a bit of a steep learning curve. As far as I know, it can handle PBC's just fine, as well as calculate hydrogen bonds. Not sure about hydrogen bonds across PB, but I assume it does that? I guess you'll have to try and see — software changes all the time anyway.
  2. MDTraj (http://mdtraj.org/): good for small trajectories, NumPy integration and quick-and-dirty analyses. Also has quite a few analysis tools, including what you need and I think it's more straightforward to use than MDAnalysis.
  3. Pytraj (https://amber-md.github.io/pytraj/latest/index.html): I haven't used this one, but apparently it can use either of the previous two for trajectory I/O, so it's more flexible in this regard. Also, it seems to support many different types of analyses (including H-bond analysis, not sure about how it handles PBC) + MPI parallelisation.

A nice summary about how these three differ, which could be somewhat outdated (but is the only thing I could find), can be found here: https://github.com/Amber-MD/pytraj/issues/445.

| cite | improve this answer | |
$\endgroup$
  • $\begingroup$ On second thought, curious if MDtraj and Pytraj handles Lammps trajectories/structure files, as that was the question originally. Will accept as answer once I know this. $\endgroup$ – gogo Aug 30 at 17:19
6
$\begingroup$

You can use OVITO as well which allows you to post-process your dump file https://www.ovito.org/

| cite | improve this answer | |
$\endgroup$
  • $\begingroup$ +1. Welcome to the site, and thank you for your contribution! We hope to see much more of you! We would appreciate if you could elaborate on your answer a bit more, because right now it's a "link-only answer" which we tend to not like. You may look around and see the typical detail level in most answers. Short answers can be left as a comment. $\endgroup$ – Nike Dattani Aug 30 at 20:56

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.