[gmx-users] rmsf

subarna thakur thakur.subarna at yahoo.co.in
Fri Oct 9 08:07:53 CEST 2009

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?


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