Re: About RMSD calculation.

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Oct 28 2005 - 16:20:48 CDT

Dear Boyang,
during the rmsd calculation, the entire structure of each frame is
fitted onto the starting structure, but this is done as a rigid fit; the
internal degrees of freedom of the frames are unaffected. This means
that the rmsd you get from the calculation ignores any drift in your
molecule, which is good; an equilibrated protein in solution should
still drift (diffuse), but should have reached an equilibrium in its
internal degrees of freedom. If you weren't performing the fitting you'd
expect the RMSD to continuously increase in accordance with the
diffusion law.

Best,
Peter

Boyang Wang wrote:

> I am doing a MD simulation for an organic molecule and need to
> determine its equilibrated configuration on the materials' surface.
> The RMSD can provide the information of whether the configuration of a
> certain molecule is "at equilibrium", by showing that the RMSD of this
> molecule compared to the initial frame is not increasing, (See tutorial).
> If the coordinates of a molecule in one frame during the simulation is
> CHANGED to superimpose its coordinates in the initial frame, and then
> could rmsd be calculated, then RMSD is not calculated for the ACTUAL
> coordinates of the molecule in each frame. So what information does
> RMSD give us?
> I wonder if you are talking about the RMSD calculation used in the
> X-Ray Structure fitting.
> Boyang
>
> */LEWYN LI <ll2150_at_columbia.edu>/* д
>
> Boyang,
>
> In order to calculate the RMSD between two structures, the program
> must first do a "best-fit" superposition of the two structures,
> and only
> then can RMSD be determined. So the coordinates of one of the
> structure
> must be changed to superimpose on the other structure, as well as
> it was
> possible.
>
> Hope this helps.
>
>
> LEWYN
>
>
> On Fri, 28 Oct 2005, Boyang Wang wrote:
>
> > Hi all. I have a basic question.
> >
> > When I load a a.psf file and its .DCD files so that I have the
> > trajectory over 3000 frames. If I type "source rmsd.tcl" in the
> TKcon
> > window, the "rmsd.tcl" script is supposed to calculate the rmsd
> of each
> > frame compared to the initial frame.
> >
> > After the calculation of rmsd, I have found that the coordinates of
> > each frame have been changed. I wonder what they have been
> changed to
> > and why are they changed.
> >
> > Thanks a lot for the time.
> >
> > Boyang
> >
> >
> > Boyang Wang,
> > Email - bwang9_at_uic.edu
> > Major - Phys. Chem.
> > dept Chemistry,
> > Univ Illinois, Chicago,
> > 60607 IL US.
> >
> > ---------------------------------
> > ŻG䣭йһʼɧų
> > Ż֡Dɱɧ
>
>
>
> Boyang Wang,
> Email - bwang9_at_uic.edu
> Major - Phys. Chem.
> dept Chemistry,
> Univ Illinois, Chicago,
> 60607 IL US.
>
> ------------------------------------------------------------------------
> ŻG䣭йһʼɧų <http://cn.mail.yahoo.com>
> Ż֡Dɱɧ <http://cn.zs.yahoo.com>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:19 CST