[gmx-users] order parameter

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Sep 1 20:35:37 CEST 2011

In addition to Justin's comment about g_order being incorrect for  
unsaturated carbons, you won't ever get numerical agreement with  
g_order, even for saturated carbons, because g_order does not use your  
explicit hydrogens. g_order uses the positions of the carbons to  
rebuild the hydrogen positions assuming perfect tetrahedral geometry,  
which you certainly don't have in all cases when you use real hydrogens.

There is a VMD tcl script that you can download that will compute  
order parameters from real hydrogen atoms. perhaps you should try to  
compare to that.


-- original message --


Thanks  lot for replying. I am doing all-atom simulation. I am doing  
the PBC before finding the angle. also I normalise the vectors before  
finding the angle.

Yes I have checked that the formula I am using for the order parameter  
is correct.
I am doing the averaging correctly.

1. I take the carbons in each tail ( I neglect the 1st and the last as  
GROMACS does) , then I find the Hydrogens associated with it.

2. Then I do the PBC , normalise them and then take the angle, then  
calculate the order parameter.

3. finally I average them over the frames.

I have gone through the procedure and still I am not getting the same  
profile as GROMACS gives.

Is there anything else that I need to include in my calculations?

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at  
gromacs.org] on behalf of chris.neale at utoronto.ca [chris.neale at  
Sent: Wednesday, August 31, 2011 8:00 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] order parameter

Dear Ramya:

Are you simulating all-atom lipids (with explicit hydrogen atoms on
the acyl chain)? If not, then you missed a step in your description of
what you have done (g_order, for example, ignores explicit hydrogen
atoms so that it can act on united atom lipids).

Not sure why PBC would be your step #3, after your step #2 was to find
the angle. I suggest that you simply run trjconv -pbc mol on your
trajectory file before you process it and then you no longer need to
worry about PBC in your custom analysis tool.

Once you have the angle, you must average it correctly. The equation
is available in most papers that describe order parameters and is
listed as a comment at the top of the gmx_order.c source file (in
version 4.0.7 at least).

If you want to get more help on your procedure after you have worked
on this for a while, I suggest laying out your procedure very
specifically. Your previous post, for example, was pretty loose with
terminology when you described your method and there is quite a bit
that one must assume.


-- original message --


I am trying to write a code for Deuterium order parameter of DOPC
lipid. I went through the code in gmx_order.c, I did the following,

1.       I took the carbons in the chain, and found its neighbors.
2.       Took the bilayer normal and found the angle between the
bilayer normal and the ?CH molecular axis.
3.       Took care of the periodic boundary conditions since I use NPT

But the code in gmx_order.c in GROMACS tries to do a lot of things
other than this, as I don?t know C or C++ language that it is using, I
don?t know what else I am supposed to include.

Can someone please help me?



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