From: Remya Ann (
Date: Fri May 04 2018 - 10:55:35 CDT

I use the 'readvarxyz' command to read multiple trajectories with varying
number/name in VMD.
I understand that the dummy atoms created are given the {0 0 0]
coordinates. But these show up in the simulation box which is not desired.
It seems as an overlapping particle.

I have 4 atom types and dummy for each gets generated in every trajectory
except the one with the maximum number of atoms. using atomselect didnt
work since I couldnt select atoms with particular coordinates. And
selecting each particle with its index is a tedious process as it changes
in each frame.

Is there a way to change the default coordinate of the dummy atom so that
it is outside the simulation box? Any sort of help is much appreciated.


Remya Ann Mathews K
Doctoral Scholar
Polymer Engineering and Colloid Science Lab
Department of Chemical Engineering
Indian Institute of Technology Madras