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: lid...@mails.tsinghua.edu.cn > ========================================= > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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. sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php