VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 30 2018 - 09:16:43 CDT

My guess is that someone just TOLD NAMD to call it a .trj, but NAMD
always outpus only a DCD file. So this can probably be solved by
simply renaming the file. Alternately, I'd want to see a hexadecimal dump
of the first 100 bytes of the file to see what the file header looks like...

Best,
  John Stone

On Mon, Oct 29, 2018 at 02:35:18PM +0000, Vermaas, Joshua wrote:
> Uhhh... What? NAMD writes .dcd files, not .trj... If NAMD wrote a .dcd
> with the wrong extension, catdcd is probably your best bet.
>
> -Josh
>
>
>
> 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
> <[1]Joshua.Vermaas_at_nrel.gov> wrote:
>
> .trj files are GROMACS, right? The trjconv utility is the usual way of
> handling this
> problem: [2]http://manual.gromacs.org/programs/gmx-trjconv.html The
> catdcd utility bundled with VMD is another
> option: [3]https://www.ks.uiuc.edu/Development/MDTools/catdcd/
>
> -Josh
>
>
>
> On 2018-10-27 08:35:47-06:00 [4]owner-vmd-l_at_ks.uiuc.edu 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.
>
> References
>
> Visible links
> 1. mailto:Joshua.Vermaas_at_nrel.gov
> 2. https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fprograms%2Fgmx-trjconv.html&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C88875ac4ffbd4c46a3ab08d63d672e2b%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636763910712527649&sdata=jAAcSn3Qxvhr1IFWXLvSqV45UNO0Jkd6MAg%2BLT6JpAg%3D&reserved=0
> 3. https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ks.uiuc.edu%2FDevelopment%2FMDTools%2Fcatdcd%2F&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7C88875ac4ffbd4c46a3ab08d63d672e2b%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636763910712527649&sdata=PZoWRYn%2BASkcwMZLpd%2Bd8GWSoYyf5%2FXxryv1B4szv2M%3D&reserved=0
> 4. mailto:owner-vmd-l_at_ks.uiuc.edu 

-- 
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/