From: Niklaus Johner (niki.johner_at_gmail.com)
Date: Wed Jul 24 2013 - 08:45:19 CDT
The electrostatic repulsion between your charged lipids is stronger when the system is not neutralized, hence the membrane expanding.
Also be careful when using PME. Your system has probably a large total charge if you didn't neutralize it and I think the use of PME in those cases should be avoided. Instead turn off PME and increase the cutoff for the electrostatic interactions. I have no experience with this, so you should definitely look in the literature or hope for someone else to give you more insight.
Weill Cornell Medical College
Harel Weinstein Lab
Department of Physiology and Biophysics
1300 York Avenue, Room D-501
New York, NY 10065
On Jul 24, 2013, at 4:37 AM, Villalain Boullon, Jose wrote:
> Dear All,
> 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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