In situations like this I would strongly recommend going back to have a close look at the structure in its original crystal environment. In the case of 2fom, it becomes clear that the disconnected loop at the top of your image is only stable due to packing against a neighbouring chain in the crystal lattice. Its association with its own chain is almost entirely via salt bridges, plus a single partially buried leucine. In solution, I'd be extremely surprised if it wasn't highly flexible. Similarly, residues 43-50 (left of your image) are only stable due to residues 43~46 binding to a crystal neighbour. So I'm not surprised at all to hear that you have a substantial amount of mobility in your simulations.

The image you've shared can not help us to understand what happened.

How did you calculate the RMSD values, I mean, respect to which coordinates you calculated the deviation values? How did you do the frame fitting?

In situations like this I would strongly recommend going back to have a close look at the structure in its original crystal environment. In the case of 2fom, it becomes clear that the disconnected loop at the top of your image is only stable due to packing against a neighbouring chain in the crystal lattice. Its association with its own chain is almost entirely via salt bridges, plus a single partially buried leucine. In solution, I'd be extremely surprised if it wasn't highly flexible. Similarly, residues 43-50 (left of your image) are only stable due to residues 43~46 binding to a crystal neighbour. So I'm not surprised at all to hear that you have a substantial amount of mobility in your simulations.

Mohd Athar Can you please share the RMSD plot? I'm pretty sure is a problem in the fitting process. You should eliminate periodic boundary condition on your system as well as fit translation/rotation movements.

hope this helps!