[gmx-users] simulation of a trimer

[Pappu Kumar]

I got a protein which undergoes conformational change during trimer formation. There is a cryoEM structure of the trimer. So I took the trimer structure and replaced one monomer with a monomer without conformational change. Then I ran a 50 ns MD md simulation with Amber99sb FF in gromacs 4.6.5, restraining two other monomers expecting to see the conformational change in the other trimer. But there was no change in the monomer structure. 

Subsequently, I made all the monomers flexible and ran 50 ns MD. Now I can see the change in monomer structure. But it has become difficult to completely align the final structure from MD with the cryoEM structure. So I am wondering what so of analysis to do in order to show that the expected conformational change is taking place. For example calculating the angle between the center of masses of the monomers, PCA, mutual information etc. I was also thinking about using MARTINI to restrain two monomers by elastic network and then perturb the other one monomer to observe changes in the system. Thank you.