From: Aron Broom (broomsday_at_gmail.com)
Date: Wed Feb 29 2012 - 16:46:05 CST
I see. I've never used steered MD, but that sounds sensible enough. You
could also consider Umbrella Sampling or Metadynamics for the same purpose
(but not having to worry about the translation) if your steered MD fails.
On Wed, Feb 29, 2012 at 5:38 PM, Jose Borreguero <borreguero_at_gmail.com>wrote:
> 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
>>
>>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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