http://manual.gromacs.org/programs/gmx-distance.html

Thanks Nik, the answer was actually in the manual. When you are prompted for an option you have to specify a pair. 

If you were used to g_dist, you can read in the page of Gromacs that in 5.0 the tool 'gmx distance' has a variation respect g_dist:

"g_dist

This tool has been removed in 5.0. A replacement is gmx distance (for most options) or gmx select (for -dist or -lt).

If you had index groups A and B in index.ndx for g_dist, you can use the following command to compute the same distance with gmx distance:

gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' -oxyz -oall

The -intra switch is replaced with -nopbc.

If you used -dist D, you can do the same calculation with gmx select:

gmx select -n index.ndx -select 'group "B" and within D of com of group "A"' -on/-oi/-os/-olt

You can select the output option that best suits your post-processing needs (-olt is a replacement for g_dist -dist -lt)"

http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0

http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0