[gmx-users] Dangling phospholipids

["Dr. Ramón Garduño-Juárez"]

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?

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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