[gmx-users] Dihedral Autocorrelation Function with negative values

David van der Spoel spoel at xray.bmc.uu.se
Fri May 31 17:39:08 CEST 2013

On 2013-05-31 15:59, Davide Mercadante wrote:
> Dear gmx users,
> I am writing to ask why I am getting a dihedral autocorrelation function
> (ACF) with negative values. I am trying to calculate the ACF using
> g_angle (gromacs 4.5.5) with the following set of flags:
> g_angle -f trajectory.xtc -type dihedral -oc acf.xvg -od angdist.xvg -n
> angle.ndx
> The ACF starts from 1 as expected and slowly drops (sometimes) to values
> below 0 (approx. -0.2). Even when I use the flag -normalize (which I
> would expect normalizes the ACF between 0 and 1) the output is identical.
> Can you please help me to figure out why this happens?
> Any help will be very much appreciated.
> Thank you in advance.
> Cheers,
> David
Because the angle between the two planes can become 180 in which case 
the dot product is negative. In the long run it should go to zero.

It is described in 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)

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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