[gmx-users] S2 order parameters

[David van der Spoel]

rams rams wrote:
> 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.

You should look for a recent paper by Alessandra Villa (J Phys Chem I 
believe) which discusses this at length.

> 
> Thanks in advance,
> Ram.
> 
> On Thu, Sep 11, 2008 at 2:30 AM, David van der Spoel 
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> 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.
> 
> 
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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 <mailto:spoel at xray.bmc.uu.se>  
>      spoel at gromacs.org <mailto:spoel at gromacs.org>   http://folding.bmc.uu.se
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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