[gmx-users] lipid order parameter

[David L. Bostick]

Pedro,

Hmm.. not sure, but intuition tells me that it is the first Scd given in
the output. I lost your message with the diagram, but I remember it
vaguely. I would imagine that g_order skips the first carbon. In which
case, you might think about including the carbonyl carbon in the index
file, but I'm not sure about the code b/c I haven't looked at it really. I
just know in principle how it works ... sorry I can't help more ... that's
all I got.

David
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David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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---------- Forwarded message ----------
Date: Fri, 25 Apr 2003 16:00:58 -0400 (EDT)
From: David L. Bostick <dbostick at physics.unc.edu>
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] lipid order parameter


Hi Pedro,

If your united atom chain contains N atoms, then you will have N-1 order
parameters.  The reason for this is that with united atoms, you have to use
C-C bond geometry to extract the angle a C-H (or for deuterium C-D) vector
would make with a stationary vector in the lab frame (in simulations the vector
is usually taken to be in the z direction) if it existed in the model.
Since you have united atoms, the angle a C-H/C-D vector makes with the
normal is not explicitly available ... This is the way the g_order code
works anyway ...

David

-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Fri, 25 Apr 2003, Pedro Alexandre Lapido Loureiro wrote:

> Hi,
>
> I am confused!
> I am simulating a DPPC bilayer and using g_order to calculate the order
> parameter (Scd).
> g_order output gives 13 Scds. DPPC has two chains, each with 14 CH2 groups and a
> terminal methyl.
> So, do those 13 values refer to the first 13 CH2 groups?
> (My guess is that they refer to the last 13, based on comparisons with
> experimental results.)
> By the way, my index files (sn2.ndx or sn1.ndx) contain the 14 CH2 plus the CH3
> groups.
>
> Thanks,
>
> Pedro.
>
> --
> Pedro Alexandre Lapido Loureiro
> Laboratório de Física Biológica
> Instituto de Biofísica
> UFRJ
> Brasil
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