VMD-L Mailing List

From: Parisa Akhski (Parisa.Akhshi_at_chem.queensu.ca)
Date: Fri Aug 27 2010 - 15:22:03 CDT

Hi,

Sorry, my mistake. I mean "name x" to define the atom name. I am not defining alignment in my script and I am not using align option in RMSDTT. So, I expect to get the same answer provided that my equation to calculate atom deviation from the reference structure (first frame) is the same as VMD.
I am actually using the equation on page 30 of the tutorial below:

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win.pdf

But, since I want to get atom deviation for each atom, I am ignoring "summation" in numerator and "/N" in denominator. Is this how RMSDTT works? Or maybe I am wrong and the numbers produced by RMSDTT when I select "... and name x" are not atom deviations for each atom?

Thanks,

Parisa

Hi,
  One potential difference between your script and the RMSDTT
plugin would be dependent on whether and how you aligned the frames
prior to computing the RMSD. It's not clear what you mean by
"atom x", as there's no such atom selection in VMD, perhaps you
meant "index x" or "serial x" or "name X"?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 27, 2010 at 02:06:40PM -0400, Parisa Akhski wrote:
> Dear VMD users,
>
> I have a question about RMSD trajectory tool on VMD.
>
> In options menu, if I select "protein and resname ... and resid ... and
> atom x", the program calculates RMSD for "atom x" for all frames and also
> gives me the "avg" for RMSD as well. Does anyone know what equation is
> used by program to get RMSD for "an atom"? Is it actually just the atom
> deviation from the reference structure and not RMSD? I have actually
> written a script to get the atom deviation for each atom and the results
> differ from what is produced by RMSDTT so, I think I need to make sure the
> equation I am using is the same as VMD first.
>
> Thanks,
>
> Parisa 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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