[gmx-users] pull code

Berk Hess gmx3 at hotmail.com
Mon Jul 19 10:06:20 CEST 2004

>From: Kay Gottschalk <kay.gottschalk at weizmann.ac.il>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: [gmx-users] pull code
>Date: Sun, 18 Jul 2004 13:13:13 +0300
>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?

If you use constraints you should use the free-energy code.
I sent a mail about this to list a month ago, including a link
to a manual with an updated pulling section:


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