[gmx-users] Dangling phospholipids

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 12 02:41:14 CET 2011

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.


> 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


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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