From: Vermaas, Joshua (
Date: Sun Oct 28 2018 - 18:01:29 CDT

.trj files are GROMACS, right? The trjconv utility is the usual way of handling this problem: The catdcd utility bundled with VMD is another option:


On 2018-10-27 08:35:47-06:00 wrote:

Dear VMD users,
      I have a problem about saving trajectory files in vmd. I have a trj file which contains about 40000 frames including water and protein structure and I want to save only protein part for all the 40000 frames. I can't just load it in vmd and save it because my system hanks. The other option is to load it in background but after loading it in background, I don't know how to save it or what is the command for saving it. Can anyone help to get out of this problem?
Thanks in advance.