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?
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