[gmx-users] g_dipole

[André Farias de Moura]

the program actually reads all frames, but it computes the correlation up to
half of the total length of the data (it is a homoscedasticity issue, you should
read some textbook on time series analysis before you increase the output
length using -acflen)

best

André

On Thu, Feb 24, 2011 at 5:04 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Nilesh Dhumal wrote:
>>
>> How can I make prog. to read all frames.
>>
>>
>
> I already answered this.  Use a proper setting for -acflen.
>
> -Justin
>
>> On Thu, February 24, 2011 2:34 pm, Justin A. Lemkul wrote:
>>
>>> Nilesh Dhumal wrote:
>>>
>>>> Hello,
>>>> I am calculating dipole autocorrelation function for my system.
>>>>
>>>>
>>>> I run the simulation for 500ps and the plot of dipole autocorrelation
>>>> function shows the results for 250 ps.
>>>>
>>>> I used the following command
>>>>
>>>>
>>>> g_dipoles -f water.trr -s water.tpr -c -corr total
>>>>
>>>> Can anyone tell whats the problem.
>>>>
>>>>
>>> This is the expected behavior.  See g_dipoles -h, especially the -acflen
>>> flag.
>>>
>>> -Justin
>>>
>>>
>>>> I am using  Gromacs VERSION 4.0.7 version.
>>>>
>>>>
>>>>
>>>> Thanks
>>>>
>>>>
>>>> NIlesh
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>> --
>>> ========================================
>>>
>>>
>>> Justin A. Lemkul
>>> Ph.D. Candidate
>>> ICTAS Doctoral Scholar
>>> MILES-IGERT Trainee
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>>
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>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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