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
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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