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

From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Feb 27 2012 - 23:15:41 CST

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 post-processing.

~Aron

On Mon, Feb 27, 2012 at 11:49 PM, kanchi subbarao rao <ksubbu85_at_gmail.com>wrote:

> 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 <ksubbu85_at_gmail.com>wrote:
>
>> 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
>> 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
>>>
>>>
>>>
>>>
>>
>

-- 
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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