From: Axel Kohlmeyer (
Date: Mon Oct 05 2009 - 20:31:13 CDT

On Mon, 2009-10-05 at 16:20 -0700, A D wrote:


this may come as a surprise to you, but proteins _do_ diffuse
in membranes. if you want to fix it you could use a weak restraint,
to the center of mass of the protein that is tied to a fixed point
in space.

it has nothing to do with the wrapping flags in NAMD.

to re-center the protein after the fact you could use
pbc wrap with using the protein as reference coordinate.
check out the pbctools plugin docs for details.


> Hello VMD Users,
> I had a simulation system where I had a membrane protein at the center
> of a bilayer. However, although I did "wrapall on", it diffused along
> the membrane (x-y plane) during my 30ns simulation. I wonder how it
> would be possible to move it back to the center of my membrane using
> VMD. Any suggestions regarding NAMD coding about how to make the
> protein stay in the center of my membrane would also be very helpful.
> Thanks a lot!!!
> Seth

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Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.