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

From: Chris Harrison (charris5_at_gmail.com)
Date: Sat Feb 25 2012 - 11:59:43 CST

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?

Best,
Chris

On Wed, Feb 22, 2012 at 2:07 PM, Jose Borreguero <borreguero_at_gmail.com>wrote:

> 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
> reply.
>
> 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
http://www.ks.uiuc.edu/Research/namd       Voice: 773-570-6078
http://www.ks.uiuc.edu/~char                          Fax: 217-244-6078

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