VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 04 2018 - 11:07:04 CDT

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.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

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.Â
> 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
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/