[gmx-users] calculation of the order parameter S2

[Mark Abraham]

Dechang Li wrote:
> Dear all, 
> 
>     I want to use g_rotacf to calculate the order parameter(S2, N-H bond in main chian).
> The tool g_rotacf needs an index.ndx file that contains two vectors. How can I make the 
> index.ndx file? Can I use the tool make_ndx to do this? Or I need to write the file manually?

See http://wiki.gromacs.org/index.php/Index_File. I think you just want
to write a file by hand.

Mark