AW: what restraint can I use to prevent membrane diffusion on the Z-axis?

From: Norman Geist (
Date: Tue Feb 28 2012 - 00:42:24 CST



maybe one could also investigate if it is a COM drift due to PME which could
be removed with zeromomentum.


Best wishes


Norman Geist.


Von: [] Im Auftrag
von Aron Broom
Gesendet: Dienstag, 28. Februar 2012 06:16
An: kanchi subbarao rao
Cc: Chris Harrison; Jose Borreguero; NAMD-l
Betreff: Re: namd-l: what restraint can I use to prevent membrane diffusion
on the Z-axis?


If your problem is like what Jose had, where the whole membrane slab is just
moving along the normal axis, I don't see why this is a problem. The system
is periodic, there will always be the same amount of water between periodic
copies, and you expect to see random diffusion in some direction. I see no
reason why you would want to restrain it under these conditions, the only
problem it will cause is a visual one which can be easily remedied with


On Mon, Feb 27, 2012 at 11:49 PM, kanchi subbarao rao <>

hi Chris,
          Is any one reply for this mail.I need to know how fix this
problem.shall you suggest me ......

On Sun, Feb 26, 2012 at 10:09 PM, kanchi subbarao rao <>

hi all
       I have also similar problem.I did some DPPC lipid bilayer
simulations.I used 3D PBC and run the simulation in NPT.
The lipid part is not diffused but it was moved along Z - axis inside
periodic Box.Due to that the water was come to one side more (at bottom )
and the other side (at top) less.I maintain the water more than fully
hydration.It means the simulation is correct. But lipid motion in along z -
axis was not looking good.
         How can we over come this problem.please any suggestions please

subbarao kanchi
physics Dept
IISC Bangalore


On Sat, Feb 25, 2012 at 11:29 PM, Chris Harrison <> wrote:

Dear Jose,


The membrane diffuses as a single unit in the z-axis? Or, you have a net
diffusion in the z-axis of all the lipids in the membrane, while the
membrane itself is not actually diffusing?






On Wed, Feb 22, 2012 at 2:07 PM, Jose Borreguero <>

Dear NAMD users,

While simulating a DLPC membrane, I noticed that it tends to diffuse along
the normal (Z-axis) component. Is there a 'standard' restrain that is used
to prevent such diffusion?
The first option I thought was to restrain the center of mass of the whole
membrane along the Z-axis, but I don't know what is a reasonable value for
the force constant.
If anyone has any experience dealing with this kind of problem, please do

Best regards,
Jose M. Borreguero


Chris Harrison, Ph.D.
NIH Center for Macromolecular Modeling and Bioinformatics
Theoretical and Computational Biophysics Group
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801       Voice: 773-570-6078 <>
Fax: 217-244-6078
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:21:41 CST