[gmx-users] g_rotacf

rams rams rams.crux at gmail.com
Sun Aug 24 16:34:53 CEST 2008


I am sorry if it is the second time I am posting the same thing. Two days
back I have posted this but myself couldnt get a copy of the mail. So I am
not very sure whether it reached the others member or not.

I want to clarify a few of the things about the usage of g_rotacf (for
rotational correlation function for molecules). In the manual it is given
like the following:

g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1 -fa expfit-x-P1
-beginfit 2.5 -endfit 20.0

I understood that -f, -s options are needed to be included in the above

It is mentioned in the manual, that the above command will calculate the
rotational function using a first order Legendre polynomial of the angle of
a vector defined by the index file.
(as I understand, -P 1 option is taking care of this. If I want to use the
second order Legendre polynomials, -P 2 will do it for me I suppose)

The above command will also fit the calculated correlation function to a two
parameter exponential (-nparm 2 is taking care of this I suppose). Does it
mean that the calculated correlation function is expressed as a sum of three
exponential terms with two variables along two directions ? What is the fit
function by default is used here ? Is it exp(-l(l+1)Di) ?

There is also an option -fitfn in the list, what are these functions are
meant for ?

-fft option is for using FFT for the computation of the correlation function
if I am correct.

-fa option I dont have any idea about it.

Thanks and Regards in advance,

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