[gmx-users] g_rotacf, order parameter S2 problem

[David van der Spoel]

Dechang Li 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:

Your simulation may be too short.
You should look at the average value of the tail over a long time.
Check J. Chem. Theor. Comp. 2 (2006) 1228
> 
> @    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
> =========================================
> 
>   
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se