[gmx-users] regarding converge of system
ahmedo047 at gmail.com
Thu Nov 1 21:42:45 CET 2012
Firstly thanks for your reply. RMSD is a measure related with whether or
not converge of particles in the structures versus the starting structure.
In other word, it is the difference (average distance) between the
positions of particles in two structures. Conformational changes is not
only on the change of the position of atoms/particles in the structure but
also depend on other parameters (dihedral angle, formation of a hydrogen
bond, tilt/rotation of a protein/peptide in a lipid bilayer, solvation
patterns, ligand binding, system volume, etc).
Am I wrong?
RMSD matrix is also used to control the convergence of the structure. What
is the main difference between RMSD and RMSD matrix?
Thanks in advance
2012/11/1 Christopher Neale <chris.neale at mail.utoronto.ca>
> 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
> 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 ).
> -- 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
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