[gmx-users] calculation of the order parameter S2

Mark Abraham Mark.Abraham at anu.edu.au
Sun Jan 4 03:38:33 CET 2009

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.


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