[gmx-users] g_rotacf, order parameter S2 problem

[Dechang Li]

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: lidc02 at mails.tsinghua.edu.cn
=========================================