From: Vermaas, Joshua (
Date: Mon Oct 29 2018 - 09:35:18 CDT

Uhhh... What? NAMD writes .dcd files, not .trj... If NAMD wrote a .dcd with the wrong extension, catdcd is probably your best bet.


On 2018-10-29 00:24:32-06:00 Sasthi Charan Mandal wrote:

Thank you for the links. The .trj files are NAMD files. So how do I do that?

On Mon, Oct 29, 2018 at 4:31 AM Vermaas, Joshua <<>> wrote:
.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.