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I obtained the rmsf graph by using the command line

cpptraj

parm solv_7zzt_chainb_noh.com1_no_water.prmtop

trajin nowatermd_7zzt_chainb_noh.com2.nc

list trajin

autoimage

atomicfluct out rmsf.bfactor @CA byatom bfactor

I have run the MD for 50 ns

Now I want to obtain an ideal graph for publication purpose .

I am attaching the graph below .Plz let me know where to rectify it in command line.

Thanks

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