What I mean by atom trajectories is the xyz coordinates of each atom at each time step. I could not find any program in the gmx package that did this, so I wrote my own. You can get it here.
From gromacs, use the trjconv program to create a series of pdb files for each time step of the simulation.
trjconv -s swnt -f traj.trr -o last.pdb -sep
swnt is the structure, traj is the trajectory file created from running a dynamics simulation and last.pdb is the name you give to the pdb series.
After running the script you get a text file for each atom the has the time and xyz coordinates:
Here is a sample output for atom 1