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
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--
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.qtp.ufl.edu
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Received on Wed May 28 2008 - 06:07:14 PDT
