From: Izhar Karbat (izhar.karbat_at_gmail.com)
Date: Mon Feb 18 2013 - 11:26:30 CST
Dear NAMD users,
I am simulating a membrane system containing an ion channel embedded in a POPC bilayer. The hydrophobic thickness of the ion channel (according to the OPM database) is 27A. The membrane patch, generated with the membrane-builder plugin has hydrophobic thickness of ca. 31A. As a result, several extracellular segments of the channel which are expected to be solvent exposed, are facing a lipid. While this does not seem to affect the simulation stability over a few ns period, i'm afraid that longer runs might get skewed by the imperfect placement of the membrane. As quite several membrane proteins deviate from the "canonic" hydrophobic thickness of ~30A, and since the membrane plugin does not offer control over the bilayer thickness,
i hope that one of you might have encountered a similar problem in the past and may share is ideas concerning possible solutions.
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