MD simulation of a protein complex with more than 600 AA residues shows an average rmsd between 1-1.5 nm. can the protein complex can be considered stable?
Besides sometimes i see a jump in the RMSD trajectories. Can it be arised due to the failure to centre the protein complex or due to the larger size of the protein.
As always, it depends. Roughly 10A may be ok for the your proteins' size. However, you should carefully review the structure and check nothing comes apart. RMSF may be useful to identify the positions with the most change. The RMSD seems also to converge soon as it stops changing much with increased simulation time. The jumps you sometimes see may arise from the protein being cut by the periodic box due to wrapping issues. What MD code do you use?
Norman Geist
I have used an online server Known as WebGro (https://simlab.uams.edu/) which uses GROMACS for MD simulation. But the same results were observed when Desmond was used for performing MD studies.
Just to add a few things over Norman Geist answer.
Do you dimer or trimer? RMSD also depends on the length of residues forming loop/unstructured region. You should check that as well.
Your complex acquired a stable structure after ~5ns and remained in the same region for the remaining length of the simulation. 3-5 A fluctuation is normal and expected, and beyond that, it should be investigated.
In my opinion, once the constrained are removed, protein acquired its natural form and stayed there. For your analysis part, try to avoid the first 10ns.