From: Vlad Cojocaru (
Date: Mon Feb 23 2015 - 04:15:44 CST

Thanks a lot Jerome and Josh,

I will give it try ...


On 02/21/2015 09:29 PM, Josh Vermaas wrote:
> 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

Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]