Dear Rout,

Have you taken the reference frame to calculate the RMSD of the structure. Before calculating the RMSD, structural deviations has to be determined to some initial crystal structure or frame at lets say 0 ns after energy minimisation. Have you done that?

Please answer these questions, then I can comment on your RMSD calculations.

Are you using PBCs? If yes, check if some parts jump through the edge of simulation box.

Just as Ali Osman Acar highlighted periodic boundary conditions (PBC) might be contributing to your problem. Please go through your trajectories by loading into either VMD or other relevant trajectory visualizer and check if such issues persist. If it does then while you extract your trajectories you may want to use -pbc nojump and subsequently in the next command use -pbc whole to overcome PBC issues.

Dear all,

Thank you very much for your valuable responses.

Dear Sashi,

I have used the frame at 0 ns for rmsd calculation and also the tpr file. But in both the cases, the results are same.

Dear Vishal and Ali,

Thank You very much. Fixing the pbc jumps worked.

Dear Rout,

Then check for PBC conditions. Check your simulation box dimenstions, cut off distances etc. These types of problem usually persists when your proteins comes out of the box and interacting with next image.