[gmx-users] on gmx make_ndx

[Brett]

Dear All,


In http://www.gromacs.org/@api/deki/files/198/=gmx-tutorial.pdf, there is



make_ndx -f run.gro
At the prompt, create a group for GLU22 with “r 22”, ARG137 with “r 137”, and then
“q” to save an index file as index.ndx. The distance and number of hydrogen bonds
can now be calculated with the commands
g_dist -s run.tpr -f run.xtc -n index.ndx -o dist.xvg


Here for g_dist, it is the distance between GLU22 and ARG137, does it mean the distance between the center of GLU22 and the cnter of ARG137? If so how does GROMACS determine the center of a residue? If I want to get the distance between one specific atom of GLU22 (for example OE2) and one specific atom of ARG137 (for example NH1), how do I specify the residue and the atom of the residue together in the make_ndx ?


I am looking forward to getting a reply from you.


Brett