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

[David van der Spoel]

On 2015-03-12 19:03, atanu das wrote:
> 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)) >
I don't think so, but please check the source code if unsure.
> 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
>


-- 
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