Dear Dr. Subhomoi Hi,Thanks a lot for your answering. I use the gmx cluster command as follow
"gmx-mpi cluster -f md300.trr -s md300.tpr -n index.ndx -cutoff 0.1 -cl cluster.pdb" , then I got a pdb file with different models of my aptamer without ligand, I need to check different interaction between aptamer and ligand during simulation time.It would be pleasure if you have any suggestion. Thanks a lot Maryam On 2019-10-05 08:43, Subhomoi Borkotoky wrote: > Hi, > > You can use "gmx cluster" to get an average structure based on RMSD. Just > use an appropriate cut-off. > > Regards, > > Subhomoi B. > > On Sat, Oct 5, 2019, 10:01 AM mmousivand93 <mmousivan...@ut.ac.ir> wrote: > >> 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. -- 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.