i done MD simulation for Free protein and Complex separately. both the structures are coming out of the box.
even i tried gmx trjconv -pbc nojumb and -center , -fit rot+trans my RMSD graph like this.
can you suggest me what is the mistake how to solve this issue. thanks in advance
make the protein as whole then fix the jump, you need to use gmx trjconv a couple of times to remove all the artifcats
please search over pbc issue, there are lots of discsion that help you to use the trjconv tool.
make an index for both chain together and center the chains first. There are no directy way, you need to play around it to get the corrected one, refer the link above.
One possibly way is to find a residue(or a atom) as close to the center of the complex and locate it in the .gro file.Using make_ndx to take it into a separate group, then center the group when using trjconv.