RMSD of what? Probably you mean RMSD from the starting (or crystal) structure. First, consider that your profile of RMSD vs. crystal structure levels off at 0.4 nm with increasing simulation time. Consider how many possible conformations are 0.4 nm RMSD away from the crystal structure. A stable RMSD does not necessarily indicate that you have obtained Boltzmann sampling of a particular conformational basin. Very generally, it is the degeneracy of RMSD with respect to conformational space that makes RMSD an insufficient indicator of convergence. There are other ways to look at this though. For instance, there might be an important degree of freedom that is important for your system but does not greatly affect the global conformation (and thus the RMSD). This might be a dihedral angle, formation of a hydrogen bond, tilt/rotation of a protein/peptide in a lipid bilayer, solvation patterns, ligand binding, system volume, etc.
Also, and I presume that this is not what Tsjerk meant (but you should check whatever reference you are referring to) it is always possible that you remain stuck within a conformational basin that is locally favourable but globally unfavourable. For other measures of convergence, first think about what you are trying to study for your system and use that to guide your selection of properties for which you can evaluate convergence. This should include both global and local structural measures. There are loads of papers available that discuss this. See papers by Grossfield, Zuckerman, and others. A colleague of mine has also shown that some properties converge faster than others (meaning that some properties, like the RMSD, converge before the partition function has converged: http://pubs.acs.org/doi/abs/10.1021/ct900302n ). Chris. -- original message -- I have two questions: 1-We can say "The RMSD is commonly used as an indicator of convergence of the structure towards an equilibrium state (Tsjerk W.)". RMSD is not sufficient to determine whether or not converge of structure/system. Why? 2-Radius of gyration, RMSD, rmsd matrix are used as an indicator of convergence of the structure. are there other indicators of convergence of the structure? Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
