[gmx-users] center of mass pulling in AFM

[Kay Gottschalk]

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 ?

Best,
Kay.