Dear Dr. David, Thank you very for the reply. When i looked the energy minimized average structure it looks just fine. ??
>>> >> I calcualted the average structure from the simulation trajectory. when >> I >> calculate the rmsd of the protein to this average sturture, it is giving >> average rmsd of 0.16 nm. But, it is not clear for me why the average >> sturcture is never adapted rmsd near (or equal) to zero. I did not >> calculate the rmsd with respect to the starting structure either. >> Any clue? > the average structure is unphysical, it may have long bonds etc. > _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
