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.
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