[AMBER] how to calculate electron density and order parameters of lipid11 membrane

From: Thomas Evangelidis <tevang3.gmail.com>
Date: Tue, 19 Nov 2013 15:33:01 +0200

Dear lipid11 developers,

I am trying to simulate a POPE bilayer in NAMD using the lipid11
parameters. For this purpose I have done some test simulations of a
hydrated POPE bilayer in a hexagonal prism box in NAMD and have measured
the Area per Lipid and Electron Density using MEMPLUGIN of VMD (upon
wrapping the coordinates
into an orthorhombic box and modifying the box vectors accordingly). The
values I got for Area per Lipid are in agreement with Skjevik et al., 2012
but the Electron Density profile deviates
(it is shifted ~ -1.3 ~1.3 e/A^3). Therefore I would like to use the same
modified version of ptraj you use to calculate these membrane attributes. I
have download if from:


but there are I couldn't find any instructions. Could someone please
instruct me how to use it to calculate the Electron Density and the SCD
Order Parameters described in the lipid11 paper?

thanks in advance,

Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens
email: tevang.pharm.uoa.gr
website: https://sites.google.com/site/thomasevangelidishomepage/
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Received on Tue Nov 19 2013 - 06:00:02 PST
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