From: Josh Vermaas (
Date: Thu Mar 26 2020 - 19:00:48 CDT

If the only thing you care about is visualization, load the pdb, clear the
bonds that are autogenerated, and go from there. In the tkconsole:

package require topotools
topo clearbonds
mol reanalyze top

If you wanted to, you could then use this loaded structure to save a
totally bogus .psf file.

set sel [atomselect top "all"]
$sel writepsf dummy.psf


On Thu, Mar 26, 2020 at 11:42 AM Borne, Vincent <> wrote:

> Hello,
> 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,
> Best,
> Vincent