[gmx-users] g_rotacf to calculate order parameter S2

Byungchan Kim bk385 at columbia.edu
Fri Jan 2 02:54:01 CET 2004

Hi Folks.

I want to calculate S2 order parameter with g_rotacf.
 From mailing list discussion, I could figure out how to use g_rotacf on my
purpose. My command is like this,
g_rotacf -f 4pti.trj.xtc -n NH_21.ndx -d -P 2
NH_21.ndx is like this
329     333

My problem is that I couldn't get the flat value of correlation function.
The simulation lasted up to 1.5 ns.
What I am curious about is whether the program use orientation of
interatomic vector "in molecular frame". Actually, I am not sure it is a
problem if the program does not use the molecular frame.
I am looking forward to hearing clever answer.

Thank you very much and Happy New Year.

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