[gmx-users] Dihedral angle autocorrelation function - g_chi function mismatch

[atanu das]

Hi again,
Just to add a note ---
It seems that g_angle can also calculate the dihedral angle autocorrelation function with the option -oc. Does this program use the same functional form as g_chi i.e. is the functions defined as ---
C(t) = <cos(theta(tau)) cos(theta(tau+t)) >
ThanksAtanu  

     On Wednesday, 11 March 2015 9:13 PM, atanu das <samrucu at yahoo.co.in> wrote:
   

 Hi All,
As Prof. David van der Spoel referred in the last communication about how the dihedral angle autocorrelation function is calculated via the program g_chi, I have a query regarding the differences that I found between the function mentioned in the article (Biophys. J. 72 pp. 2032-2041 (1997)) and the function used by the program g_chi.
According to the article, the dihedral angle autocorrelation function is defined as:
C(t) = <cos[theta(tau)-theta(tau+t)]> ..... (Eq. 1 of the article)

However, the g_chi program uses the function:
C(t) = <cos(theta(tau)) cos(theta(tau+t)) > ..... (Eq. 2)
So, apparently the g_chi program uses a different function. Am I correct? Is there a way around it? I mean is there a way to estimate C(t) using the function given in the article (Eq. 1)?
ThanksAtanu 
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