[gmx-users] writing trajectory of an atom

[Salman Zarrini]

Hadi,

Anyway, you need the group of that single atom in your index.ndx file and
as you pointed out yourself the ``xtc-grps = single-atom'-group' flag will
do the job for you if you grompp -n index.ndx where the single-atom-group
presents in the index file.

Cheers,
Salman

On Tue, Dec 17, 2019 at 7:20 PM Hadi Rahmaninejad <ha.rahmaani at gmail.com>
wrote:

> Hi Salman
>
> Thanks, but in this way I will save trajectory of all of the atoms in the
> trr file, and then I extract just the trajectory of my atom. However, what
> I need is to avoid savimg lots of data. I needed an option in my mdp input
> file. Do you have any idea for that?
>
> Thanks
> Hadi
>
> Sent from my iPhone
>
> > On Dec 17, 2019, at 5:37 PM, Salman Zarrini <salman.zarrini at gmail.com>
> wrote:
> >
> > Hi Haid,
> >
> > In your index file, you should first generate a group which contains only
> > the atom of your interest:
> >
> > gmx mak_ndx -f case.gro -o index.ndx
> >> a atom
> >> q
> >
> > Then you can extract the trajectory of that single group (single atom)
> > using:
> >
> > gmx trjconv -f traj.xtc -n index.ndx -o atom.xtc
> >> choose the group of your interest here!
> >
> > Regards,
> > Salman
> >
> > On Tue, Dec 17, 2019 at 4:04 PM Hadi Rahmaninejad <ha.rahmaani at gmail.com
> >
> > wrote:
> >
> >> Hello Dear gromacs users,
> >>
> >> To reduce the size of my xtc file, I need to just extract the
> trajectory of
> >> a especial atom, which is not an independent group, it is just one atom
> in
> >> a group. I know that in md options I can narrow down trajectory of a
> group
> >> (xtc_grps = XXX), but for just one atom or molecule in that group I
> cannon
> >> find. I appreciate if any user can give me some hint,
> >>
> >> Thank you,
> >> Hadi
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>