[gmx-users] Dangling phospholipids
"Dr. Ramón Garduño-Juárez"
ramon at fis.unam.mx
Wed Feb 9 18:21:47 CET 2011
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?
Waiting for your replies...
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