From: Vlad Cojocaru (
Date: Sat Feb 21 2015 - 03:59:33 CST

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 ?


Best wishes

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]