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

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Sun Feb 26 2012 - 10:39:42 CST

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.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
India

On Sat, Feb 25, 2012 at 11:29 PM, Chris Harrison <charris5_at_gmail.com> 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?
>
> 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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