I have run MD simulation of a protein-protein docked complex for 50ns. The RMSD plot obtained from the simulation is attached here.
The RMSD plot shows a stable trajectory for entire simulation, except for 46-47 ns when there is a huge fluctuation.
What could be the possible reason of such fluctuation and how to improve this?
Any suggestion is highly appreciable.
Thanks in advance.
RMSD involves the superposition of the sampled conformations against a reference one (I assume it is the initial quaternary structure in this case). This superposition implies bringing together the centers of mass of the system (every sampled conformation and the initial one) and a rotation to overlap the inertia moments (vectors) defined by the system atoms. If, for example, the two proteins separate a little bit, or one of them slightly changes orientation, the center of mass and/or the vectors change, and the superposition yields a huge RMSD value, even though the conformations are not so different. You should be able to notice it, though, by watching at the simulation movie.
- Badges
- Science topic
- Similar topics
- Heat