[gmx-users] a residue move in extremely large scale in MD

[Mark Abraham]

On 6/08/2012 8:58 PM, Acoot Brett wrote:
>   Dear All,
>
> I have a protein with about 400 amino acids. I have done a production MD of it. I find in the 400 amino acids, there is 1 amino acids, during the whole MD process, this residue moves in a extremely large scope in comparison with all the other residues.
> Do you think this single residue with extremely large-scale movement in the whole MD has important biological function, or has no biological function?

I'd start by proving that it was not a problem with periodic boundary 
conditions! If real, movement may or may not be indicative of functional 
significance - the question is impossible to answer out of context.

Mark