[gmx-users] how to distance between COM of two groups of atoms?

[Ming Tang]

Thank you Justin,

I set 2 groups (start and end )in index.ndx file. each group has 3 alpha carbon atoms. I used the following command to calculate the distance between COM of those 2 groups

gmx distance -n index.ndx -select 'com of group "start" plus com of group "end"' -f test.pdb -s topol.tpr -oxyz dist.xvg

and got average distance:4.385, which is not correct as my protein is around 30-nm-long.

is the command I used correct?