Re: Membrane Simulations

From: Anshu Bhatia (ciphurus_at_gmail.com)
Date: Tue Oct 28 2008 - 12:31:55 CDT

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 - 15:48:31 CST