Re: About RMSD calculation.

From: Boyang Wang (
Date: Fri Oct 28 2005 - 15:55:41 CDT

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.


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

Hope this helps.


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 -
> Major - Phys. Chem.
> dept Chemistry,
> Univ Illinois, Chicago,
> 60607 IL US.
> ---------------------------------
> ŻG䣭йһʼɧų
> Ż֡Dɱɧ

Boyang Wang,
Email -
Major - Phys. Chem.
dept Chemistry,
Univ Illinois, Chicago,
60607 IL US.

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