[gmx-users] center of mass pulling in AFM

[Berk Hess]

>From: Kay Gottschalk <kay.gottschalk at physik.uni-muenchen.de>
>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] center of mass pulling in AFM
>Date: Mon, 17 Jul 2006 12:58:02 +0200
>
>Hi there,
>
>we are doing pulling simulations of protein complexes. For these  
>simulations, we keep the COM of one group fixed and pull on the COM  of the 
>other group. Now we got into this discussion, whether this  introduces 
>artificial distortions on the hold protein. If the protein  deforms into 
>the direction of the force vector, the center of mass  changes. Does this 
>mean that a force on the other end of the protein  is applied, so that the 
>other end also deforms in order to keep the  center of mass fixed? Or how 
>is the COM held fixed ?

This all depends on what you are keeping fixed.
Of which groups are you keeping the COM fixed?
Since MD preserves momenta, you can only
fix distances between COMs by adding forces,
which is exactly what the pull code does.
Additionally fixing more than one COM will
introduce additional forces.

Berk.