You need to use the flag -res, if not the default is measured by atom.

Cheers

I've just found a solution for this:

just need to add flag -res , so the command would be:

gmx rmsf -f md_noPBC.xtc -s md.tpr -o rmsf.xvg -res

then choose C-alpha as a group for rms calculation

You have to create an index:

$ gmx make_ndx -f md_0_10.tpr -o index_ca.ndx

Choose

> 1 & 3

22 Protein_&_C-alpha : 347 atoms

Then, calculate RMSF as follows:

gmx rmsf -s md_0_10.tpr -f md_0_10_center.xtc -n index_ca.ndx -o rmsf_protein.xvg

You need to use the flag -res, if not the default is measured by atom.

Cheers

Thank you! M. Florencia Martini

For atomic level

gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg

and for residue

gmx rmsf -f md_0_1.xtc -s md_0_1.tpr -o rmsf.xvg

change .xtc and .tpr file name accordingly.