[gmx-users] S2 order parameters

[rams rams]

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
<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.
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