[gmx-users] center of mass pulling in AFM
gmx3 at hotmail.com
Tue Jul 18 11:31:34 CEST 2006
>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
>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.
More information about the gromacs.org_gmx-users