[gmx-users] center of mass

[Qi Sun]

My simulation system is polymer dissolved in Cyclohexane ( totally 674 
molecules) and N,N - dimethylformamide (totally 500 molecules). When I 
trying to calculate the diffusion constant or the radial distribution 
function. I would like to consider the whole molecule as single super atom. 
Right now the index file can consider each atoms as separate points, I am 
more interested in the whole molecule together. Is there a algorithm 
somewhere can solve this problem?
Thank you in advance for any comment or ideas.
Best regards