[gmx-users] Dangling phospholipids

[Justin A. Lemkul]

Dr. Ramón Garduño-Juárez wrote:
> Justin,
> 
> Regarding my question I forgot to tell you that after expanding the 
> system 4X, we have performed 26 shrinking steps at the 0.95 rate.
> 
> The system we are working with is one in which we have embedded two 
> proteins into the bilayer, one of them is a toxin and the other a 
> putative channel. Both proteins are docked in some way.
> 
> The last lines of the last shrinking step are:
> -------
> Area per protein: 10 nm^2
> Area per lipid: 0.596104455536294 nm^2
> 
> Area per protein, upper half: 9 nm^2
> Area per lipid, upper leaflet : 0.612233487794359 nm^2
> 
> Area per protein, lower half: 8.5 nm^2
> Area per lipid, lower leaflet : 0.620298003923391 nm^2
> 
> Writing Area per lipid...
> Done!
> -----
> 
> The area per lipid of DMPC has been reported to be between 0.40 to 0.703 
> nm^2, with an average value of 0.656 nm^2
> 
> After visualizing of the system we found a that those lipid molecules at 
> the four corners of the box as disordered. That is, one of their tails, 
> or both, are far from the core of the bilayer. Nothing like the original 
> lipid box.
> 
> Do you think that we have shinked too much, or as you said, we have not 
> minimized long enough?
> 

That's possible.  InflateGRO tends to overestimate the true area per lipid, so 
your DMPC may be compressed a bit more than you think.  I usually stop DPPC 
compression in the ballpark of 0.70 nm^2.  If the lipids are reasonably close to 
the rest of the system and not completely isolated in their own vacuum state, 
then a gentle equilibration can bring everything together within a few ns.

-Justin

> Cheers,
> Ramon Garduno
> 
> 
> 
> El 09/02/2011 11:25 a.m., Justin A. Lemkul escribió:
>>
>>
>> Dr. Ramón Garduño-Juárez wrote:
>>> Dear All,
>>>
>>> First of all I want to tank Justin Lemkul and Thomas Piggot for their 
>>> useful comments that helped me to resolve my previous questions 
>>> regarding the construction of a lipid membrane.
>>>
>>> Now I would like to post this question to this forum.
>>>
>>> I got through placing a putative ion channel into a DPPC bilayer. I 
>>> managed to expand this sytem -> minimize it -> shrink it (several 
>>> times) -> minimize it (several times) until I got an adequate lipid 
>>> density.
>>>
>>> After viewing the final results I noticed that there are several 
>>> lipid molecules that are dangling at the end of the periodic box.
>>>
>>> Is this normal, or I did something wrong?. If this is expected, How 
>>> do I get rid of the dangling lipid molecules before I start a MD 
>>> simulation?
>>>
>>
>> By "dangling" do you mean that they are somewhat isolated from the 
>> rest of the lipids?  If so, how many are there?  Usually this just 
>> indicates that you're not done shrinking the membrane back to 
>> appropriate dimensions.  The final box vectors achieved through 
>> shrinking should usually be fairly close to the original dimensions of 
>> the system.  If this is not the case, then you're not done building 
>> your system.
>>
>> -Justin
>>
>>> Waiting for your replies...
>>>
>>> Sincerely,
>>> Ramon Garduno
>>>
>>

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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