[gmx-users] writing trajectory of an atom

[Hadi Rahmaninejad]

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
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