[gmx-users] RMSD

Justin Lemkul jalemkul at vt.edu
Wed Jan 23 19:06:06 CET 2013

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 



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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