[gmx-users] Conformation search!

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 18 16:37:32 CEST 2008

Anthony Cruz wrote:

>  > You seem to want to let your domains move relative to each other, but
>  > also to deny them much internal freedom. So what you want to do is
>  > enforce (some of) their internal structure. Thus, use distance 
> restraints.
>  >
>  > Mark
> Thank you for your answer. But probably I don't make my point clear. I 
> have a protein with two units (domains). I think that distant restraint 
> will restraint the distance between the two domains or units... This is 
> done by the linkers between them. I want them to move freely but not to 
> change its structure, like freezing the backbone and let the rest to 
> move freely.
> How I could do this?

Distance restraints to "enforce their *internal structure*"... So don't 
restrain all the distances, just some cunningly chosen ones inside each 


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