[gmx-users] Dangling phospholipids

Justin A. Lemkul jalemkul at vt.edu
Wed Feb 9 18:25:58 CET 2011

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.


> 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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