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

From: kanchi subbarao rao (ksubbu85_at_gmail.com)
Date: Tue Feb 28 2012 - 11:58:49 CST

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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