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

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Mon Feb 27 2012 - 22:49:02 CST

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
>>
>>
>>
>>
>

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