[gmx-users] order parameters is more than one

[Karim Mahnam]

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 (https://extras.csc.fi/chem/
courses/gmx2007/analysis/):

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
>q

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.
Thank you very much

On Fri, Dec 23, 2016 at 9:54 PM, Karim Mahnam <karimmahnam93 at gmail.com>
wrote:

> 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 (https://extras.csc.fi/chem/
> courses/gmx2007/analysis/):
>
> 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
> >q
>
> 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
>