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
<[EMAIL PROTECTED] <mailto:[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.
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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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