From: Axel Kohlmeyer (
Date: Fri May 04 2018 - 11:17:19 CDT

On Fri, May 4, 2018 at 12:07 PM, John Stone <> wrote:
> Hi,
> I'm not familiar with the "readvarxyz" command you refer to. Is this a
> script you're using? Where did you get it? That's not a built-in command
> in VMD.


readvarxyz is a subcommand of the topotools package.


all dummy atoms are flagged with a value of -1.0 in the user field
(others have 1.0). so if you create a selection of "user > 0", VMD
will not show any dummy atoms at all.
if you still want to move them to a different location, you can use
VMD scripting, and create atom selections based on the user field as


> Best,
> John Stone
> On Fri, May 04, 2018 at 09:25:35PM +0530, Remya Ann wrote:
>> Hi,
>> 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.Ā
>> 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.
>> Thanks,
>> --
>> Remya Ann Mathews K
>> Doctoral Scholar
>> Polymer Engineering and Colloid Science Lab
>> Department of Chemical Engineering
>> Indian Institute of Technology Madras
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Phone: 217-244-3349

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.