Re: Membrane Simulations

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Tue Oct 28 2008 - 14:19:12 CDT

Hello Anshu,

Here is a classic reference:
http://dx.doi.org/10.1016/0304-4157(89)90010-5

Best,
Jerome

On Tue, Oct 28, 2008 at 1:27 PM, Anshu Bhatia <ciphurus_at_gmail.com> wrote:
> Thanks for the reply and references, Vlad. I am trying different protocols
> now. As a related question to what we discussed:
> What are the various lipid properties which can be monitored to find out if
> or not a lipid bilayer is properly
> equilibrated. I know about RMSD and perhaps Area per Lipid. What are the
> other properties (order parameters?)
> which can be observed. Also, how to find the experimental values of Area per
> lipid. Is there a common source where
> properties for various lipids is listed. Again, I would be very thankful to
> get references.
> Anshu.
>>
>> On Thu, Oct 23, 2008 at 3:06 AM, Vlad Cojocaru
>> <Vlad.Cojocaru_at_eml-r.villa-bosch.de> wrote:
>>>
>>> Dear Anshu,
>>>
>>> Although I am not that experienced, I believe using NVT over NPT in the
>>> melting phase ensures that the bilayers which are far from equilibrium do
>>> not collapse before being properly solvated in the head-group region and
>>> before the tails acquire their intrinsic disorder. However, its not clear to
>>> me why shouldn't be correct to start directly with NPT especially if you
>>> have membranes which are far from equilibrium such as those created with
>>> VMD. Also, the melting with fixed head groups is done sometimes even before
>>> solvation. If you have resources maybe you should simply try different
>>> protocols. Its always the best solution when you are not sure. Also, its
>>> nice to find such answers by yourself than from others. If you do not have
>>> time and resources, than probably best is to stick with what is the most
>>> documented.
>>>
>>> Constant area (or NPgammaT - adding surface tension) is used during
>>> production runs because all currently available all-atom force fields for
>>> lipids do not lead to a nicely equilibrated area per lipid. The
>>> equilibration is very long and it generally leads to an area per lipid which
>>> is smaller than the experimental value. Now, of course keeping the area
>>> constant in the simulation adds stress to the simulation. How this affects
>>> your results its not clear. There is literature on the topic so better read
>>> it before deciding. Its also not clear whether it is really better to run
>>> with an artificially kept constant area or in NPT with smaller area per
>>> lipid than the experimental value. It is common sense that one should follow
>>> more membrane properties than just the area per lipid to decide.
>>>
>>> I guess for a start take a look at:
>>> Kandt et al, Methods 41 (2007) 475488
>>> Gullingsrud J and Schulten K, Biophysical Journal Volume 86 June 2004
>>> 34963509
>>>
>>> and references therein ....
>>>
>>> Hope this helps a bit
>>> vlad
>>>
>>>
>>>
>>> Anshu Bhatia wrote:
>>>>
>>>> Hi,
>>>> I asked this question on the forum before but did not get a satisfactory
>>>> response so far. Let me try and rephrase my question.
>>>>
>>>> I am trying to study the spatial variation in lipid bilayer properties
>>>> due to the presence of a gramicidin channel in the middle of the bilayer.
>>>> Because a gramicidin channel is smaller in length than the lipid bilayer
>>>> thickness, I expect the bilayer to shrink near the channel, but retain
>>>> its normal thickness far away from the channel.
>>>>
>>>> I need help in developing a protocol for my specific problem. From the
>>>> protocols I have seen so far, I have 2 questions for the protocol:
>>>>
>>>> (1) All protocols seem to constrain the head groups of lipids for a
>>>> short period of the time and let the lipid tails melt before letting the
>>>> whole system evolve.
>>>> This melting is done to interlace the lipid chains without changing the
>>>> thickness. In some protocols this melting is done in NVT ensemble.
>>>> What is the reason to choose NVT over NPT?
>>>>
>>>> (2) After this melting is performed most protocols use an NPT ensemble
>>>> with constant area or constant ratio for production runs.
>>>> Why is constant area used? In my case, I am interested in looking at the
>>>> variation in properties of lipid across the space, should constant ratio
>>>> still be used.
>>>>
>>>> P.S.: If anyone can provide me with a good reference paper which
>>>> discusses issues about lipid simulations in namd, I would be very thankful
>>>>
>>>> Anshu.
>>>>
>>>
>>> --
>>>
>>> ----------------------------------------------------------------------------
>>> Dr. Vlad Cojocaru
>>>
>>> EML Research gGmbH
>>> Schloss-Wolfsbrunnenweg 33
>>> 69118 Heidelberg
>>>
>>> Tel: ++49-6221-533266
>>> Fax: ++49-6221-533298
>>>
>>> e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
>>>
>>> http://projects.villa-bosch.de/mcm/people/cojocaru/
>>>
>>>
>>> ----------------------------------------------------------------------------
>>> EML Research gGmbH
>>> Amtgericht Mannheim / HRB 337446
>>> Managing Partner: Dr. h.c. Klaus Tschira
>>> Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter
>>> http://www.eml-r.org
>>>
>>> ----------------------------------------------------------------------------
>>>
>>>
>>
>
>

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:50:01 CST