[gmx-users] g_rotacf

[Xavier Periole]

On Thu, 4 Sep 2008 09:45:34 -0400
  "rams rams" <rams.crux at gmail.com> wrote:
> 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:
Well if you do not get an answer that is probably that your post is not
really asking a quick "answerable" question and you might want to
re-formulate your post or dig a bit to make things easier.
> 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 ?
This is an old exemple ... a bad one! Those options do not seem to exist
anymore! Never knew they existed!
you can grep "\-nparm" and "\-fa" in tools/*.c and you'll see they
only appear in gmx_rotacf.c
anyways These things are probably taken care of more invisibly.
-nparm seems to give the number of parameters in the function to fit
-fa the function to fit

now: -nparm do not exist and -fa is -fitfn, most likely!

This exemple should be removed and replaced! Just look at the options\listed 
when you type g_rotacf -h.
> Also do we need to use -fitfn option to obtain the rotational auto
> correlation functions ??
No, -fitfn defines the type of function you'd use to fit the correlation
function, which itself is written cause -o rotacf.xvg ...

XAvier.
> 
> 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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-----------------------------------------------------
XAvier Periole - PhD

Molecular Dynamics Group / NMR and Computation
University of Groningen
The Netherlands
-----------------------------------------------------