AMBER Archive (2008)

Subject: Re: AMBER: mass weighted rms fit

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sun May 25 2008 - 11:26:11 CDT

Dong:

The basic idea of mass weighting is to differentially take into account
how much each atom moves, based on its mass. Basically, what affects a
system more, a H atom moving 1 Angstrom or a C atom moving as much ?
Clearly the 'heavier' atoms affect structure and dynamics more.

In the case you describe, the difference between mass-weighted and not
mass weighted RMSD is relatively minor. The masses of those atoms are
12, 14 and 16, not a huge difference. In cases where people do CA RMSD,
there is of course no mathematical difference between mass-weighted and
not mass weighted RMSD.

So, there is a scientific reason to use mass-weighted RMSD but in your
case it would not matter much numerically.

Cheers
a.

Dong Xu wrote:
> Hi All,
>
> I have a question about mass weighted rms fit in ptraj. It is said
> mass weighted rms fit is recommended than not. What's the advantage to
> have mass weights in the alignment process, say, the selection atoms
> are backbone, CA, C, N, O?
>
> Thanks!
>
> Dong Xu
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
> 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu