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Hi,<br><br>I would say rotational acf's can be negative.<br>In most cases this will indicate bad sampling.<br>This is not suprising considering the extremely long times you printed.<br>I guess you get positive values for shorter correlation times.<br><br>Berk<br><br>> From: X.Periole@rug.nl<br>> Subject: Re: [gmx-users] g_rotacf, order parameter S2 problem<br>> To: gmx-users@gromacs.org<br>> Date: Wed, 14 Jan 2009 12:23:11 +0100<br>> <br>> On Sun, 11 Jan 2009 12:50:00 +0800<br>> Dechang Li <li.dc06@gmail.com> wrote:<br>> > Dear all, <br>> > <br>> > I used g_rotacf to calculate the order parameter (S2, N-H bond in <br>> > main chian). Thanks to Xavier Periole's advice, I make the index file<br>> > and obtained some results. However, some results I got made me puzzling<br>> > that the order parameter is negative! Here is one of my results:<br>> > <br>> > @ title "Rotational Correlation Function"<br>> > @ xaxis label "Time (ps)"<br>> > @ yaxis label "C(t)"<br>> > @TYPE xy<br>> > ...<br>> > 119944.000 -0.16902<br>> > 119946.000 -0.16845<br>> > 119948.000 -0.16812<br>> > 119950.000 -0.16845<br>> > 119952.000 -0.16834<br>> > 119954.000 -0.16825<br>> > 119956.000 -0.16875<br>> > 119958.000 -0.16823<br>> > 119960.000 -0.16850<br>> > 119962.000 -0.16885<br>> > 119964.000 -0.16892<br>> > 119966.000 -0.16924<br>> > 119968.000 -0.16885<br>> > 119970.000 -0.16928<br>> > 119972.000 -0.16889<br>> > 119974.000 -0.16901<br>> > 119976.000 -0.16866<br>> > 119978.000 -0.16901<br>> > 119980.000 -0.16895<br>> > 119982.000 -0.16953<br>> > 119984.000 -0.16932<br>> > 119986.000 -0.16961<br>> > 119988.000 -0.16947<br>> > 119990.000 -0.16890<br>> > 119992.000 -0.16952<br>> > 119994.000 -0.16986<br>> > 119996.000 -0.16970<br>> > 119998.000 -0.16941<br>> > 120000.000 -0.16908<br>> > <br>> > <br>> > The command I used is : g_rotacf -s Order.tpr -f Order.trr -d -n index.ndx <br>> >-P 2 -nice 0 .<br>> > Actually, when I used the option "-P 1", the negative results appear <br>> >similarly. <br>> > Before I calculated the S2 parameter, I removed the rotation and <br>> >translation movement of <br>> > the molecule using the tool trjconv. <br>> > Is that the negative results reasonable? <br>> No! the order parameter must be between 0 and 1. Considering the length<br>> of your simulation (120 ns) most of the NH vectors will have sampled<br>> enough for you to get a reasonable value. However some of them will not<br>> and it also depends on the topology of your protein.<br>> You should look at the curve and try to make sense with its shape.<br>> Undulations are typical of lack of convergence. Note that in some cases<br>> it is very difficult to obtain a smooth curve. Eg. we had to run ~1000<br>> cases and average them to get a acceptable curve. You do not need to<br>> do that but be aware that it is not always trivial to get a C(t) converged.<br>> Anyways, a negative value without undulations would indicate that you<br>> did something wrong somewhere. May be in the fitting procedure.<br>> <br>> XAvier.<br>> > <br>> > <br>> > <br>> > Best regards,<br>> > 2009-1-11<br>> > <br>> > <br>> > ========================================= <br>> > Dechang Li, PhD Candidate<br>> > Department of Engineering Mechanics<br>> > Tsinghua University<br>> > Beijing 100084<br>> > PR China <br>> > <br>> > Tel: +86-10-62773574(O) <br>> > Email: lidc02@mails.tsinghua.edu.cn<br>> > =========================================<br>> > <br>> > <br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -----------------------------------------------------<br>> XAvier Periole - PhD<br>> <br>> - Molecular Dynamics Group -<br>> Computation and NMR<br>> University of Groningen<br>> The Netherlands<br>> -----------------------------------------------------<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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