On Sun, 11 Jan 2009 12:50:00 +0800
Dechang Li <[email protected]> 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: [email protected]
=========================================
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-----------------------------------------------------
XAvier Periole - PhD
- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands
-----------------------------------------------------
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