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?
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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