From: Villalain Boullon, Jose (jvillalain_at_umh.es)
Date: Wed Jul 24 2013 - 03:37:20 CDT
I have looked for similar questions in the mailing list but I have not found any response to my doubts.
I am trying to set up a system containing a peptide (out of the membrane), a membrane containing negatively charged phospholipids and water. The system is either neutralized or not and I want to check the possibility of the peptide to insert in the membrane under those conditions.
First question. The system, when composed of the membrane containing negatively charged phospholipids without being neutralized, expands in the xy direction. The same system but neutralized does not expand (using the same conf file). I suppose that it should be possible to set "useconstantarea" to "yes" to avoid the spreading, but I have a question: would it be such a system and condition reliable in biological terms?.
Second one, following the first. If I set "useconstantarea" to "yes" I suppose that the peptide would never insert in the membrane, even if the peptide, because of its hydrophobicity, tends to insert into it. Is that supposition right?.
Third, following the second. If I can not set "useconstantarea" to "yes", which is the parameter I should use to maintain the membrane without spreading in the xy direction ?.
Many thanks in advance,
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