[gmx-users] g_rotacf

[rams rams]

Hi Xavier,

I am extremely sorry for incomplete information. But this is a follow up to
my previous two emails. Unfortunately I havent received any suggestions for
them and it appears like you too missed them. For more clarity I am pasting
them here again:



Dear users,

To calculate the rotational auto correlation functions, the command
mentioned in the maual is:

g_rotacf -P 1 -nparm 2 -fft -n index -o .xvg -fa  -beginfit -endfit

what are the -nparm and -fa options are meant for ?

Also do we need to use -fitfn option to obtain the rotational auto
correlation functions ??

Ram.





Dear users,

I have given a command like the following to calculate the rotational auto
correlation function:

 g_rotacf -f .trr -s .tpr -P 2 -fft -o .xvg -b 0000 -e 10000  -n .ndx -d

I want to use the second order Legendre polynomial to fit. I integrated the
resulting .xvg file, to obtain the correlation time using:

g_analyze -f .xvg  -integrate

The output is the following. Could some one help me in understanding it
betterly.

Calculating the integral using the trapezium rule
Integral 1   120.92840  +/-    0.00000
                                      std. dev.    relative deviation of
                       standard       ---------   cumulants from those of
set      average       deviation      sqrt(n-1)   a Gaussian distribition
                                                      cum. 3   cum. 4
SS1   2.428352e-02   2.972849e-02   4.204243e-04       9.301   120.228


Which value corresponds to correlation time and in which units (its in ps I
suppose) ?

Thanks in advance.

Ram.


On Thu, Sep 4, 2008 at 2:32 AM, Xavier Periole <X.Periole at rug.nl> wrote:

> On Wed, 3 Sep 2008 23:40:14 -0400
>  "rams rams" <rams.crux at gmail.com> wrote:
>
>> Hi,
>>
>> I am so surprised for not finding any one who have better experience with
>> g_rotacf. I have been playing around with it and the time correlation
>> value
>> I got by g_rotacf is so small in comparison to the time correlation value
>> I
>> calcualted using the hydrodynamic radius of the protein. The value is
>> nearly
>> 10 times less. Can some one give me a better idea about g_rotacf.
>>
> Many people have certainly used g_rotacf to get ACFs of different
> observables.
>
> Anyways the way you describe your system, command line and your problem
> does
> does not help anyone to help you. Read your message above and think about
> what
> you would answer! You've played around with g_rotacf therefore you know it
> is not straightforward to give you the magic command.
>
> XAvier.
>
>>
>> Ram.
>>
>
> -----------------------------------------------------
> XAvier Periole - PhD
>
> Molecular Dynamics Group / NMR and Computation
> University of Groningen
> The Netherlands
> -----------------------------------------------------
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