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

[Rabeta Yeasmin]

Hi Bhupendra,

Thanks for your reply. The RMSD is actually 3.5nm means 35A, which seems
very large compared to the RMSD of that protein in all-atom simulation
which is mostly between 5-6A. I have checked the trajectory as you
suggested, My system is a dimer protein inside a lipid bilayer and it looks
like if I remove the pbc effect using the following command
*gmx trjconv -s 0A.gro -f 0A-2.xtc -o 0A-2-pbc.xtc -pbc nojump -ur compact
-n index-all.ndx*

the protein structure get stretched all the time  which causes the RMSD to
be so high all-the time. If I use the original trajectory, the RMSD is
usually 0.9nm to 1.5nm except when the protein encounter pbc effect. I am
wondering how can I remove pbc effect without stretching the protein and
keeping the dimer as a whole.

Thanks.
Rabeta Yeasmin