[gmx-users] choosing group of atoms in trjconv

[Irem Altan]

Hi,

I’m trying to get coordinates of the Protein-H group from a .trr file with trjconv. I do the following:

echo 2 | gmx trjconv -f all.trr -s nvt.tpr -o out.pdb

Is there a way to get rid of the echo command and pass the information that I want the second group with a flag to trjconv, somehow?

Best,
Irem