Hello everyone,

I have run an MD simulation on a protein using Gromacs, and converted the .xtc file to .pdb using the following command

gmx trjconv -f md.xtc -s md.tpr -o protein.pdb -dt 1000 -pbc nojump

And also converted the .xtc file to .dcd using mdconvert to be able to do analysis in Bio3d in R.

In Bio3d, my RMSD graphs looks like this...

I used to following code in R to get this graph:

dcd_100