[gmx-users] g_order problems

[paloureiro at biof.ufrj.br]

> Thank's a lot your quick replay, but I my case I have the following chains
> that contain insaturations:
>  
> -O-(O=)C-(CH2)7-CH=CH-(CH2)7-CH3
>  
> Can I still use g_order with the unsaturation??? Which is the first carbon I
> have to put in the index file the one in the ester or the first CH2? Its
> important the order of the carbons in the the index file? My molecule has two
> diferents chains, then I have to construct an index file for each or I can
> put all in the same file?
>  
> Thanks in advance Hector
>  


Regarding the unsaturation, there is an option -unsat in g_order... but I have 
never "played" with it...
The first group is the first CH2.
I think the order of the groups is important...
Regarding the last question, it depends on you want to see. The experimental 
data is obtained for a specific chain (sn1 or sn2), at least for DPPC and 
DMPC... Why don`t you create separate files and see if the results are 
different...

Regards.

Pedro.