Dear friends,

I have a question regarding to the conformation change of a protein, say protein's conformation at different temperatures, different solvent environments, and the difference between a potein conformation in bulk water solution and the potein conformation on surfaces...

As I know, RMSD, is potentially one of the properties to represent that. But how to calculate that? Anyone can provide me the subroutine for calculating this property?

Or we may superimpose the two structures to have a comparison.

Any other properties? Or software, free package, helpful websites and any other suggestion?

Thank you very much for your reply.

zjnjuct