[gmx-users] correlation function

Justin A. Lemkul jalemkul at vt.edu
Sun Aug 23 03:17:44 CEST 2009

Jamie Seyed 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?


> 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.


> 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.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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