Dear David, I tried to calculate the S2 order parameters using g_rotacf. I removed the rotational and translational degrees of freedom from my trajectory using:
trjconv -f -s -o -fit rot_trans Then used this new trajectory to calculate the correlation functions using g_rotacf: g_rotacf -f -s -o -P 2 -d -n -noaver The index file contains N-H bond vectors and the simulation I ran is for 50 ns. The decay of the correlation function is smooth and after a while it is pleatue (parallel to time axis). I averaged the second half of the correlation function values for each vector. I think these corresponds to the S2 order paramters. But a few of them turned out to be negative which are not supposed to be I believe. Is there any reason for this or am I making any mistake in the process. Thanks in advance, Ram. On Thu, Sep 11, 2008 at 2:30 AM, David van der Spoel <[EMAIL PROTECTED]>wrote: > rams rams wrote: > >> Dear users, >> >> The S2 order parameters obtained by using g_chi, are they corresponds to >> the Lipari_Szabo NMR order parameters for characterizing the internal >> motions? >> > No, they are described here: > > D. van der Spoel and H.J.C. Berendsen: Molecular dynamics simulations of > Leu-Enkephalin in water and DMSO Biophys. J. 72 pp. 2032-2041 (1997) > >> >> Also it is mentioned in the manual that the obtained S2 parameter >> corresponds to a dihedral and the generated plot is residue vs S2. Does it >> mean that the S2 parameters are averaged on each residue ?? >> > No, you have one values for each dihedral. > >> >> Thanks in advance. >> Ram. >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 [EMAIL PROTECTED] >> 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. > [EMAIL PROTECTED] [EMAIL PROTECTED] 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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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