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

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Wed Feb 29 2012 - 16:38:44 CST

Dear Aron,

What you say makes sense, but I want to compute the work done by the
pushing force as I insert the peptide into the membrane (steered MD).
Hopefully I'll get some free energy profile as a function of insertion
depth. Hence I need the membrane to stay in place.

Jose

On Tue, Feb 28, 2012 at 5:46 PM, Aron Broom <broomsday_at_gmail.com> wrote:

> Honestly I don't think that is needed. I understand that you could
> restrain some of the lipids, and then apply some kind of constant force to
> the peptide, but I suspect that it is much better and easier to justify, if
> you just apply an attractive force between the peptide and some portion of
> the membrane. That way you are considering the relative distance between
> them and net translation is irrelevant.
>
> But who knows, maybe I'm out to lunch.
>
>
> On Tue, Feb 28, 2012 at 2:50 PM, kanchi subbarao rao <ksubbu85_at_gmail.com>wrote:
>
>>
>>
>> ---------- Forwarded message ----------
>> From: kanchi subbarao rao <ksubbu85_at_gmail.com>
>> Date: Tue, Feb 28, 2012 at 11:28 PM
>> Subject: Re: namd-l: what restraint can I use to prevent membrane
>> diffusion on the Z-axis?
>> To: Aron Broom <broomsday_at_gmail.com>
>> Cc: Namd Mailing List <namd-l_at_ks.uiuc.edu>
>>
>>
>> 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
>>>
>>>
>>
>>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
>
>

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