[gmx-users] Calculating C-alpha RMSD for coarse grained simulation

[Rabeta Yeasmin]

Hi,

I am new user of GROMACS. I have run coarse-grained umbrella sampling
simulation in GROMACS. I had prepared the system in CHARMM-GUI. After
running the simulation, now I want to calculate the RMSD of the protein. I
have used the following command to remove pbc effect first-
gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
-n index-all.ndx

And then used the following command to calculate the RMSD-

gmx rms -s step6.0_minimization.tpr -f 0A-2-pbc.xtc -fit rot+trans  -o
rmsd-2 -pbc

But after running the command, it asks to select group of least square fit,
I choose protein and the RMSD value is too high around 3.5 nm. Can you
please help me how I can calculate RMSD for coarse grained protein?

Thanks.

Rabeta Yeasmin