I am trying to calculate RMS fluctuation's in the position of few atoms of polypeptide. After reading trajectory (dcd file) when I use COOY DYNA COMP, it generates average structure over entire trajectory and puts it into comparison set. If I want to calculate RMS fluctuation not over entire trajectory but over some desired small portion of full trajectory, I want to have average structure generated over exactly on that particular portion of full trajectory. Is there any way to generate such an average structure??