[gmx-users] protein unfolding in water

[fatemeh ramezani]

dear users

I'm studying gold nano-particle effect on one of the blood protein stability and structure. one time I simulated the protein in the presence of  the gold nanoparticle and once without nanoparticles.

when I simulated protein alone in water, I expected the protein to remain stable but protein RMSD, gyration,dssp and .... graphs show protein structure is changing and protein helices are opening during the simulation.  

 Thus, I can not study nanoparticle interaction effect on the protein structural changes , because the structural changes also observed  in the absence of nanoparticle.
I think there is a problem. What is the solution you offer me? What is the problem? 

sincerely

Fatemeh Ramezani