From: Borne, Vincent (
Date: Thu Mar 26 2020 - 12:07:21 CDT


I am currently trying to use VMD to visualize and render some trajectories of a molecular dynamic simulation that I made. The problem is that, since I am making a coarse grained approach of my biological system, the particles that I am creating are not strictly biological materials, and thus I can't use the automatic psf builder to be able to visualize the .dcd file that I created to track a few particles of interest.

I was able to create a (working) simple pdb file with a minimum information in it but there is not reason to state that the different particles inside my simulation are are bonded in any way. To simplify everything I just stated that my particles were hydrogen (but I also tried with carbon and oxygen) moving freely in my system, on their own.

Do you know of a simple way that I may have not seen, to visualize the trajectories of my particles inside vmd (using my .dcd file or any other format that would not require a psf file that you can think of)? If not is there a way to create a "dummy" psf file that would allow me to visualize my trajectories without having to build a completely accurate chemical structure around it?

I can basically get any kind of trajectories file out of my code since I have all the coordinates of all my particles for every frames.

Thank you a lot in advance for any help that you might provide,