[gmx-users] Order parameters of lipid

[Justin A. Lemkul]

minnale wrote:
>  
> I want to calculate order parameters of palmitoyl and oleyl chains of 
> POPC which ran it for 5ns, so I have done below mentioned steps.
> 1. First I tried for Palmitoyl, so I made .ndx file by using make_ndx 
> command and selected a C34|a 035|a C36.....a C50.
> In index file the palmitoyl chain selected like this C34_O35_C36......C50
> 

You need the index groups to specify each atom separately, and only include 
carbon atoms.  Your index group will be something like:

[ C34 ]
(atoms)
[ C36 ]
(atoms)
etc.
[ C50 ]

> 2. This index file feed to g_order command
>     g_order -f .xtc -s .tpr -n palmit_ord.ndx -o order -od scd.xvg -unsat

There are no unsaturated carbons in a palmitoyl chain.

-Justin

>   This programming is running very slowly
> Have I done any mistake here?
> I would be thankful for your help
>  
> 
> 
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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