[gmx-users] rmsf

Justin A. Lemkul jalemkul at vt.edu
Fri Oct 9 12:33:59 CEST 2009

subarna thakur wrote:
> Hello
> I want to analyze the RMSF fluctuation of each residue of a protein 
> during a simulation run. I am giving the command
> g_rmsf -f md.xtc -s md.tpr -b 4000 -e 6000 -o traj_rmsf.xvg -ox 
> traj_avg.pdb. Then I am selecting the whole protein for the analysis. I 
> am getting the RMSF per atom in the .xvg file and I have to plot the 
> graph as RMSF versus atom no. but I want  to have the RMSF of each amino 
> acid residue.How Can I get the RMSF of each residue , what is the 
> command for that?

Have you looked at g_rmsf -h?  I suspect you'll find something useful.


> Subarna
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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