From: Norman Geist (
Date: Mon Mar 07 2016 - 01:07:22 CST

Generally a trajectory does only contain coordinates. An atom name is _NOT_ a time dependand property, therefore you might want to write your atom indices to a simple text file to do whatever you want to do with it later.


Norman Geist


Von: [] Im Auftrag von Sangkha Borah
Gesendet: Freitag, 4. März 2016 20:56
Betreff: vmd-l: printing out trajectories with some random indices of atoms renamed frame by frame


Dear all,


          I have a situation in which I need to identify random atoms/molecules (not same set of indices) and print them out with some other names like X, Y, Z etc. I can identify easily those indices at every frame using vmd tools, based on distance/angle criteria and print them out separately, but it will not serve my purpose. Instead I want to keep all the atoms in the trajectory and only rename the particular selected atoms only, keeping all the other informations unchanged.

          I think I have to use "rename" command in vmd, but I am not able to figure out how to use it! Perhaps if I use a selection to rename, it will preserve the information and rename those chosen indices of atoms for the frames to follow as well. I certainly do not want to do that.


            Is there any other ways as well that might be useful ? Please help!

Thank you very much in advance.


Best regards,

Sangkha Borah
IIT Guwahati, Assam, India