[gmx-users] rot_correlation

rams rams rams.crux at gmail.com
Thu Oct 9 22:55:12 CEST 2008

Dear Xavier,

I am sorry for posting an email which is not directly related to the

I have created a trajectory which contains the time dependent orientational
changes of my reference structure (from the original trajectory generated by
gromacs). I obtained the average rotational correaltion function of a few
selected vectors from the newly generated trajectory. From these I wanted to
obtain the average correlation times by fitting the generated correlation
function to a function.

I have looked at the literature aswellas a couple of recently published
papers (JCTC, 2006, 2, 1228), the total correlation function is separated as

C(total) = C(rot) * C(int)

here, C(rot) can be fitted to 1/5 * exp (-t/t_c); where "t_c" is the
correlation time.

My question is:

If I use this function, when t=0, the function will have a value of 0.2 and
how can I use this function to fit the rotational correaltion function
(where, I have a decay starting from 1 when t=0). If I dont use the 1/5
scaling factor, the fit is good and I obtained the correlation time as 0.96
ns. ( I really dont have any idea whether it is low or high).

I also wanted to know, after a couple of nano seconds, the correlation
function becomes -ve. What these -ve correlations mean ?

Thanks and Regards,
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