Use "gmx distance -n index.ndx -f traj.xtc -s topol.tpr -oav -oall" with index file write in this way: 

[CA_1 - CA_2]

300 402

I know VMD can do it but I was looking for some gromacs post-processing programme which can do it easily. Sometimes VMD crashes due to memory issues when you supposed to upload huge trajectory files.

Use gmx distance (g_dist in old versions) with index groups specifying the atoms of interest. It's very straightforward.

Use "gmx distance -n index.ndx -f traj.xtc -s topol.tpr -oav -oall" with index file write in this way: 

[CA_1 - CA_2]

300 402

The atoms need to be in separate groups, not together, e.g.

[ CA_1 ]

300

[ CA_2 ]

402

Not necessarily if you choose right group

How does one calculate the distance between a single group? The gmx distance syntax requires a selection to be made. If you choose the same group, which contains the same atoms, twice, the distance between their COMs is zero.

gmx distance calculates distances between pairs of positions as a function of time. Each selection specifies an independent set of distances to calculate. Each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc.

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

How to calculate the distance of center of mass between two groups? 

I select two groups and it appears the error like this:

Inconsistency in user input:

Selection 'a_1-627' does not evaluate into an even number of positions (there

are 627 positions)

Thank you for your help.

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