[gmx-users] order parameters is more than one

Karim Mahnam karimmahnam93 at gmail.com
Fri Dec 23 19:24:45 CET 2016

Hello GMX users
I want to calculate order parameters (S2) for NH bonds of backbone of one
protein.  I did 20 ns MD simulation and performed these commands according
to Proof Van der Spoel comments (

1-gmx trjconv -f md.trr -s md.tpr -fit rot+trans -o norot.trr  -nice  -20
Select 'Protein'  group

2-gmx make_ndx -f md.tpr -o n1.ndx
> a N H & !r 1  *
##* is number of proline residues
>name 19 NH

3-gmx rotacf -s md.tpr -d -n n1.ndx -P 2 -f norot.trr -noaver  -o
rotacf.xvg -nice  -20  -dt 400
Select 'NH'  group

4- ./process_rotacf.pl rotacf.xvg

But autocorrelation numbers for each amino acid and order parameters for
each amino acid was more than one.

Would you please tell me what is my error and whow can I solve this problem.
I attached  S2.xvg file to this mail.
Thank you very much

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