Getting forces within a distance cutoff of an index atom : gmx traj

User discussions
1

GROMACS version:2016.5
GROMACS modification: No
Hi all ,
I am using gmx traj to get all the forces on the index atom with the following command
gmx traj -s %s_md.tpr -f %s_md.xtc -n probe.ndx -of %s_probeF.xvg

How can I get the all the force within a certain distance cutoff from my index atom?
For example instead of forces due to all the atoms in the box, I want forces within 10 angstrom of my index atom.
Thanks in advance.

2

gmx traj only prints out the forces that were already computed by mdrun. If you want only forces acting on an atom within 10 Å then I suggest specifying plain cutoffs (no long-range algorithms) in a new .mdp file and using mdrun -rerun to re-evaluate energies and forces.