[gmx-users] Dangling phospholipids

"Dr. Ramón Garduño-Juárez" ramon at fis.unam.mx
Wed Feb 9 18:21:47 CET 2011

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?

Waiting for your replies...

Ramon Garduno
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