From: John Stone (
Date: Fri Mar 27 2020 - 00:16:37 CDT

  You can also add the parameter "autobonds off" when loading a file
of this sort so you don't have to clear any guessed bonds later.

  John Stone

On Thu, Mar 26, 2020 at 06:00:48PM -0600, Josh Vermaas wrote:
> 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
> -Josh
> On Thu, Mar 26, 2020 at 11:42 AM Borne, Vincent
> <[1]> 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
> References
> Visible links
> 1.

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