[gmx-users] regarding converge of system

[Tsjerk Wassenaar]

Hi Ahmet,

The RMSD is the Cartesian distance between two points in conformational
space. Like the distance between Siirt and Istanbul (1600km) is not the
average between the north-south distance and the east-west distance. It's
the norm of the difference vector, the square root of the sum of the
differences in each dimension. Nothing more, nothing less.

An RMSD matrix is a matrix in which each element m_ij is equal to the RMSD
of the structures i and j. For 100 structures, you get a 100x100 matrix,
with all diagonal elements equal to zero.

Cheers,

Tsjerk


On Thu, Nov 1, 2012 at 9:42 PM, ahmet yıldırım <ahmedo047 at gmail.com> wrote:

> Dear Christopher,
>
> 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
> > 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
> > --
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>
>
>
> --
> Ahmet Yıldırım
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada