[gmx-users] writing trajectory of an atom

[Salman Zarrini]

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
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