[gmx-users] correlation function

[Jamie Seyed]

On Sun, Aug 23, 2009 at 10:30 AM, Jamie Seyed <jamie.seyed at gmail.com> wrote:

> Hi Justin,
> Thanks for the answers. Please check below...
>
> On Sat, Aug 22, 2009 at 9:17 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
>>>
>>> On Sat, Aug 22, 2009 at 8:44 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>> jalemkul at vt.edu>> wrote:
>>>
>>>
>>>
>>>    Jamie Seyed wrote:
>>>
>>>        Hi Justin and Mark,
>>>        Thanks. Actually I made a mistake and it seems going to the zero
>>>        (even negative!)
>>>        --But I wanted to know how I can write my command to get only
>>>        one graph (average of all instead of all of them). I read the
>>>        manual chapter-8 and by average I mean I should get one curve
>>>        starting at 1 and coming down to zero...I also tried
>>>
>>>
>>>    That's not an average; that's the shape of the ACF curve.
>>>
>>>  Yes I need to get that shape using g_analyze..!.
>>>
>>
>> Right, I just don't understand why you think you need to obtain some sort
>> of average.  What do you mean by "all of them"?  How many graphs are there?
>
>
> Actually when I open autocorr.xvg I can see from data/feature extraction/
>  the last set is S1295 (N=101, autocorr.xvg) which means they are 1296
> graphs each with poor statistics start at 1 and coming down. To have a ACF
> for a system I expect to get one graph with good statistic... I hope I make
> it clear now.
>
>>
>>
>> <snip>
>>
>> No, only ACF based on coordinates. I read from the list that people said I
>>> can use g_rotacf  -d for calculation of correlation functions...and actually
>>> I did it for a simple system. But for new system using another index file it
>>> is complaining.
>>>
>>>
>> Then I don't think g_rotacf is the tool you want.  There is no magic way
>> to simply calculate some sort of general correlation function.  You
>> calculate an ACF from the specific data you have.  So if you're interested
>> in some sort of position-dependent data, then rotational properties may or
>> may not be relevant.
>>
>> You can certainly use g_rotacf if you think it will be meaningful; see
>> below regarding your .tpr file.
>>
>> <snip>
>>
>> tpbconv  -s f.tpr  -f f.trr  -n f.ndx  -o tpxout.tpr
>>>
>>>
>>
>> Don't use -f.  If you do, tpbconv will think you are trying to create a
>> new .tpr file that starts off from the time frame present in the .trr file.
>
>
> Yes I removed -f and I got  tpxout.tpr and used it for g_rotacf
> g_rotacf  -f f.xtc  -s tpxout.tpr  -n f.ndx  -o rotacf.xvg  -d
> but the result I got is like y=2x that starts at (0,0) which y=C(t) and
> x(Time,ps). Which is very strange... I don't understand what are these
> results using this command. (I should mention that f.xtc contains the
> coordinates of selected atoms). Many thanks for your attention and your
> help/Jamie
>

Please ignore this part since I used wrong files.../Thanks, Jamie

>
>
>>
>> -Justin
>>
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> 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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>
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