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

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Tue Feb 28 2012 - 13:30:16 CST

I restrained a few lipid atoms located in the membrane rim and now the
membrane stays put.

Later I will be forcing a peptide into the membrane and I don't want it to
move as a result of the peptide pushing the lipids aside. I hope the
restrains will do the trick :)

Jose

On Tue, Feb 28, 2012 at 12:58 PM, kanchi subbarao rao <ksubbu85_at_gmail.com>wrote:

> well thanks again,
> I checked in vmd mailing-list, I don't find
> discussion on imaging in VMD.If it possible in VMD then my problem is
> solved. I will try how to do in VMD. If anybody know how to do
> imaging in VMD ,could you suggest me
>
>
>
> thanks
> subbaro kanchi
>
>
> On Tue, Feb 28, 2012 at 11:12 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>
>> Well, I think VMD might be more powerful than ptraj. Basically you'll
>> just have to tell it where you want the center of the box to be, and it
>> will wrap things around the periodic boundaries accordingly.
>>
>> I'm not sure of the exact command, as I've never really been that
>> concerned about it, but it is certainly something you can do.
>>
>>
>> On Tue, Feb 28, 2012 at 12:29 PM, kanchi subbarao rao <ksubbu85_at_gmail.com
>> > wrote:
>>
>>> Thank you for reply
>>>
>>>
>>>
>>> >> which can be easily remedied with post-processing.
>>> I did imaging in by using amber tool (ptraj). But The structure is still
>>> not changing.I used .psf file instead of topology and provided box
>>> information in input file of ptraj.
>>>
>>> could you give any suggestion to get good visualisation .
>>>
>>>
>>> subbarao kanchi
>>>
>>> On Tue, Feb 28, 2012 at 10:45 AM, Aron Broom <broomsday_at_gmail.com>wrote:
>>>
>>>> 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
>>>>
>>>>
>>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>>
>

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