[gmx-users] still g_order problem!

[Alan Dodd]

You need a seperate group for each carbon atom along
the chain... You can average multiple chains by
letting each group have equivalent atoms from multiple
chains, but unless you have at least 3 groups in your
index file, you'll never get an order parameter out. 
Search through the mailing list archive, this has been
described in some detail a couple of times.

--- Rongliang Wu <wurl04 at iccas.ac.cn> wrote:

> Hello gmx-users,
> 
> 	i have made a index file of carbon atoms as
> follows:
> [ CAE ]
>    5   15   25   35   45   55   65   75   85   95 
> 105  115  125  135  145 
>  155  165  175  185  195  205  215  225  235  245 
> 255  265  275  285  295 
>  305  315  325  335  345  355  365  375  385  395 
> 405  415  425  435  445 
>  455  465  475  485  495  505  515  525  535  545 
> 555  565  575  585  595 
>  605  615  625  635  645  655  665  675  685  695 
> 705  715  725  735  745 
>  755  765  775  785  795  805  815  825  835  845 
> 855  865  875  885  895 
>  905  915  925  935  945  955  965  975  985  995 
> 
> and used the command "g_order -f traj.trr -s
> dwmd.tpr -szonly -n -sl 8" to calculate the order
> parameters of atoms in the index file, but the
> results are all 0 for each slices. but the system
> was apparently not amorphous. are there any possible
> mistakes for my procedure.
> 
> 
> yes,the order parameters calculated in the previous
> method are average over time and molecules.the order
> parameters can also be calculated (and are all 0 for
> each slices) if i put all carbon atoms in the index
> file. what this order parameter  will be? average
> over atoms?  
> 
> Thanks!
> 
> Regards!
>                     
> Sincerely,
> 
> Rongliang Wu
> State Key Laboratory
> of Polymer Physics and Chemistry
> Center of Molecular Science
> Institute of Chemistry
> Chinese Academy of Sciences
>  				
> 
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡wurl04 at iccas.ac.cn
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2006-02-07
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