VMD-L Mailing List

From: Sasthi Charan Mandal (sasthi.phys_at_gmail.com)
Date: Tue Oct 30 2018 - 10:01:08 CDT

Thank you, Mr. John Stone and Vermass Joshua. Yes, I just named it as .trj
and after that I renamed it .dcd.

On Tue, Oct 30, 2018 at 7:46 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/
>