[AMBER] Lipid Order Parameters

From: somdev pahari <somdevpahari1.gmail.com>
Date: Sat, 6 Oct 2018 20:33:48 +0530

Hi All,

I want to calculate Acyl Chain Order Parameters from Lipid Simulations.
Basically I calculated it with two different ways. One is using 'lipidscd'
and another is using 'vectormath'. For later case I define ucellz as a
first vector
and specific C-H as a second one (say C12 and H2R) for a particular chain
(say sn1). Then determine order parameter by using formula
Scd = 1/2 * < 3(cos(theta)^2) - 1 > from a single pdb file containing only
one frame.
I want to know that are these two ways reflects the same thing or not?
Because I got two different values for these two different ways.
I am afraid that probably I messed up all the things for determine from
theta to Scd. That's why I am asking.

Kindly give me suggestion
Thanks in advance
Somdev Pahari
Research fellow
National Institute of Technology, Rourkela
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Received on Sat Oct 06 2018 - 08:30:03 PDT
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