RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints )

From: wmsmith (
Date: Wed Jun 29 2005 - 13:43:44 CDT

It might be possible to prevent the center of mass from drifting using a Tcl
script. The script would have to calculate the net acceleration of the center
of mass due to the forces acting on the constituent atoms. Then apply an equal
acceleration in the opposite direction by proportionally distributing force to
each atom based on the atom's mass. This would prevent any net acceleration of
the center of mass of the membrane.
Alternatively, a constant velocity SMD with a velocity of zero set for each
membrane atom may be sufficient as well
>===== Original Message From Sascha Tayefeh <>
> Hi all,
> there have been quite a few postings to this topic here (see
>"constraining center of mass...", Feb 17 2005, or "can i restrain the
>center of molecule...", Apr 20 2004), which have remained unanswered.
>Facing similar problems, I'd like to give it another try:
> I've desperatly been trying to find a way adding planar restraints to a
>membrane/protein simulation in order to avoid water molecules
>penentating the membrane. In order to do so e.g. in Charmm, one would
>use its so-called MMFP (Misc. Mean Field Potential) commands. What would
>be the workaround in NAMD?
> Further, I would like to prevent drift of the membrane during
>production run by referring to the center of mass of the complete
>membrane rather than restraining each of the membrane's atom. How to do
> Last, I need to define a cylindrical potential function to prevent
>drift of the protein. Any idea?
> Thank you for any suggestions!
> Sincerly
>Sascha T.

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