[gmx-users] RMSD

[Justin Lemkul]

On 1/23/13 12:48 PM, Shima Arasteh wrote:
> I want to find the structure with the lowest RMSD, so I think it does not make different to set any of pdb files as the ref structure.
> I made an attempt and got the RMSD regarding the first pdb file. The RMSD relative to -1 for the ref structure, is written in xvg file. Is my approach logically correct?
>

The RMSD value should be positive, so I don't know how you get -1.  Your 
approach does not seem very sound - a structure does not have an absolute RMSD 
value; it has an RMSD value relative to a reference structure, which must be 
some sort of meaningful comparison or else you're not really measuring anything 
useful.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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