From: Kay Gottschalk <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@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.
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