[gmx-users] How constraint structure not conformation

Anthony Cruz acb15885 at uprm.edu
Wed Apr 16 16:17:59 CEST 2008

Hi User:
We have a protein with two domains. This two domains were connected by two 
linkers of different length. We want to study the different conformation that 
the protein domains can adopt depending the length of the linkers without 
loosing the secondary structure feature present. I was thinking in use some 
position restrain in the backbone atoms of the domains  and leave the linkers  
and all the side chains to move freely but this aproach will not let the 
system to change the conformation. 
I'm using GROMACS 3.2.1.
With a dihedral constraint it will be posible to what I want to do?
How can I do it?
There is any other option to do this?

Best Regards,

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