Re: [AMBER] Lipid Order Parameters

From: Daniel Roe <>
Date: Wed, 10 Oct 2018 12:07:20 -0400


On Sat, Oct 6, 2018 at 11:05 AM somdev pahari <> wrote:
> 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.

1) You need to average over *all* C12-H2R bonds.
2) The lipidscd calculates the angles with respect to the Cartesian
axes (basically assuming your membrane is aligned with the axes).
3) You need to make sure you are using the 'dotangle' mode of
'vectormath' to ensure the vectors are properly normalized.

Hope this sheds some light on your issue,


> 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
> Odisha
> India
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Received on Wed Oct 10 2018 - 09:30:03 PDT
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