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?
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