[gmx-users] pull code

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Sun Jul 18 12:13:13 CEST 2004

In the system I am working with, there are data indicating that a 
conformational change occurs upon ligand binding which can be enforced 
(without ligand) by introducing a disulphide bridge that can only be 
formed in the ligand-bound conformation. I didn't see the 
conformational change when just doing a (10 ns...) simulation, probably 
because it's too slow. Now I'd like to slowly pull the disulphide 
bridge-forming atoms together, in the presence and absence of ligand, 
and compare the force profile/energy profile. I think the pull code 
should be able to do so, but somehow I can't figure it out from the 
manual how to really do it. One workaround would be to make many 
consecutive simulations with shortening distance restraints, 
equilibrate the system for each distance and then measure the 
constraint force with free energy perturbation. But that seems rather 
tedious. Does anyone know a better approach? Perhaps I can do 
AFM-pulling and stop at a certain distance?

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