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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
