[gmx-users] how to calculate average structure

[mmousivand93]

Dear all; 

I performed a molecular dynamic simulation(50ns) for a complex
aptamer-ligand and I am going to analysis the interaction between
aptamer and ligand during the simulation,then I will need the average
structure. How can I calculate the average structure, is it correct to
use the following command "GMX DCOVAR –F TRAJ.XTC –S TOPOL.TPR –B 801 –E
1000 –AV <OUT-PUT-FILENAME>.PDB" , when I used the command, I should
select two group as "THE LEAST SQUARES" and "COVARIANCE ANALYSIS", which
group must be selected,aptamer or system or ligand? 

Thanks a lot