[gmx-users] S2 order parameters

David van der Spoel spoel at xray.bmc.uu.se
Thu Sep 11 08:30:28 CEST 2008

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.
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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

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