[gmx-users] g_rotacf, order parameter S2 problem

[Xavier Periole]

On Sun, 11 Jan 2009 12:50:00 +0800
  Dechang Li <li.dc06 at gmail.com> wrote:
> Dear all, 
> 
>    I used g_rotacf to calculate the order parameter (S2, N-H bond in 
> main chian). Thanks to Xavier Periole's advice, I make the index file
> and obtained some results. However, some results I got made me puzzling
> that the order parameter is negative! Here is one of my results:
> 
> @    title "Rotational Correlation Function"
> @    xaxis  label "Time (ps)"
> @    yaxis  label "C(t)"
> @TYPE xy
> ...
> 119944.000    -0.16902
> 119946.000    -0.16845
> 119948.000    -0.16812
> 119950.000    -0.16845
> 119952.000    -0.16834
> 119954.000    -0.16825
> 119956.000    -0.16875
> 119958.000    -0.16823
> 119960.000    -0.16850
> 119962.000    -0.16885
> 119964.000    -0.16892
> 119966.000    -0.16924
> 119968.000    -0.16885
> 119970.000    -0.16928
> 119972.000    -0.16889
> 119974.000    -0.16901
> 119976.000    -0.16866
> 119978.000    -0.16901
> 119980.000    -0.16895
> 119982.000    -0.16953
> 119984.000    -0.16932
> 119986.000    -0.16961
> 119988.000    -0.16947
> 119990.000    -0.16890
> 119992.000    -0.16952
> 119994.000    -0.16986
> 119996.000    -0.16970
> 119998.000    -0.16941
> 120000.000    -0.16908
> 
> 
> 	The command I used is : g_rotacf -s Order.tpr -f Order.trr -d -n index.ndx 
>-P 2 -nice 0 .
> Actually, when I used the option "-P 1", the negative results appear 
>similarly. 
> 	Before I calculated the S2 parameter, I removed the rotation and 
>translation movement of 
> the molecule using the tool trjconv. 
> 	Is that the negative results reasonable? 
No! the order parameter must be between 0 and 1. Considering the length
of your simulation (120 ns) most of the NH vectors will have sampled
enough for you to get a reasonable value. However some of them will not
and it also depends on the topology of your protein.
You should look at the curve and try to make sense with its shape.
Undulations are typical of lack of convergence. Note that in some cases
it is very difficult to obtain a smooth curve. Eg. we had to run ~1000
cases and average them to get a acceptable curve. You do not need to
do that but be aware that it is not always trivial to get a C(t) converged.
Anyways, a negative value without undulations would indicate that you
did something wrong somewhere. May be in the fitting procedure.

XAvier.
> 
> 
> 
> Best regards,
> 2009-1-11
> 
> 
> ========================================= 
> Dechang Li, PhD Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> PR China 
> 
> Tel:   +86-10-62773574(O) 
> Email: lidc02 at mails.tsinghua.edu.cn
> =========================================
> 
>  
> 
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-----------------------------------------------------
XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-----------------------------------------------------