[gmx-users] index file for DPPC

[Justin A. Lemkul]

koukoulitsa at eie.gr wrote:
> Dear all gmx_users,
>  
> I want to calculate the order parameter after the incorporation of a 
> molecule of DHA in the DPPC Bilayer (100 DPPC lipids).
>  
> I have read in the manual that the program can gives an idea of the 
> ordering of a molecule from head to tail and I have read that I have to 
> construct an index file, but I don't know how I can group all the CH2 
> segments that are necessery for this calculation.
>  

There is an exact how-to on the wiki site:

http://wiki.gromacs.org/index.php/make_ndx

-Justin

> I will appreciate your help,
>  
> thanks in advance!
>  
> Caty. 
>  
>  
>  
> Dr. Koukoulitsa Catherine
> Laboratory of Molecular Analysis
> Institute of Organic & Phamaceutical Chemistry
> Hellenic National Research Foundation
> Vas. Konstantinou 48
> 11635, Athens
> Greece
>  
> Tel: +30-210-7273869-71
> Fax: +30-210-7273872
> Web: www.eie.gr <http://www.eie.gr>
> 
> 
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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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