[gmx-users] RMSF or RMSD per residues

[Justin A. Lemkul]

shiva birgani wrote:
> Dear all
> I want to analyze the mobility of residues in various conditions.
> I need to know  examining the RMSF is more useful or RMSD per residue?

That depends on your definition of "mobility."  If you want to determine 
fluctuations/flexibility, then RMSF will have meaning.  If you're looking simply 
for structural deviations/changes, then perhaps RMSD is appropriate.  You can 
gather both using a single g_rmsf command, so draw your own conclusions from 
what you obtain.

-Justin

>  Thanks in advance
> Shiva
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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