From: Villalain Boullon, Jose (jvillalain_at_umh.es)
Date: Thu Oct 17 2013 - 07:44:47 CDT
I have been looking for a similar problem in the forum, but I have been unable to find an answer for the problem I have.
I am using the NAMD membrane tutorial to guide me in the simulation of a system composed of a relatively hydrophobic peptide and a membrane (POPC). We know, as observed experimentally, that the peptide inserts into the membrane, probably located at the membrane interface (observed through IR, DSC and fluorescence). I would like to study the insertion of the peptide into the membrane as well as its location; however, until now and after several nanoseconds the peptide remains always in the water phase. The peptide is unconstrained, I have used either constant pressure or constant pressure and area, PME and a temperature of 310K.
Perhaps I should increase the temperature to a higher one as I have read in some works or I should increase steadily the temperature, but I do not know which is the next step I have to do in order to observe the penetration of the peptide into the membrane.
Could you give me some suggestion about the steps I should do?. Thanks a lot in advance.
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