[gmx-users] rmsd of the same protein

[QZ]

Dear All,
 I have done an 8ns MD on a protein. MD was stable and equlibrated. I 
took frames between 2ns and 8ns and run g_clusters to an average 
structure. I also minimized the average structure. Now I compare this MD 
structure with its crystal structre. The RMSD is 1.5 Angstrom for the 
backbone. The big RMSD's are at loops and termini. Are these two 
structure considered the same?

Qin