From: Josh Vermaas (
Date: Sat Feb 21 2015 - 14:29:49 CST

Hi Vlad,

I'm not sure if there is a more straightforward way of doing it, but
this is what I would do:

1.) Make a temporary pdb with as many dummy atoms as you want
2.) use topotools to merge together this set of dummy atoms with your
original structure
3.) Populate the new larger structure from your original psf and dcd
4.) Write out the new data to either a psf/dcd pair or a js file, which
contains everything in a single file.

Is there a particular reason you want to store the dummy atoms as atoms?
Normally, I save things I'm interested in to a numpy array, since I
don't intend to visualize it with VMD.

-Josh Vermaas

On 02/21/2015 03:59 AM, Vlad Cojocaru wrote:
> Dear all,
> I would like to take a trajectory, calculate the coordinates of some
> centers of mass in each frame and add these as dummy atoms into new
> PSF and DCD files. These new files would then contain both the
> original atoms and the new dummy atoms.
> I looked into doing this with VMD but did not find a solution yet. Can
> anyone give me an advice on whether this is possible whatsoever ?
> Thanks
> Best wishes
> Vlad