[gmx-users] order parameter

[chris.neale at utoronto.ca]

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.

Chris.

-- original message --

Hi,

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  
ensemble.

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?

Ramya