[gmx-users] correlation function

[Justin A. Lemkul]

Jamie Seyed wrote:
> Hi Mark,
> Thanks for the answers. I want to use g_analyze but it needs a file 
> graph.xvg as an input file. How can I get that for calculation 
> of auto-correlation function? Many Thanks in Advance/Jamie
> 

The graph.xvg file contains the data for which you want to obtain the 
autocorrelation function.  Many of the Gromacs analysis tools produce .xvg files 
of whatever quantity they are measuring.  I suppose it would then be important 
to figure out what type of data you are trying to obtain the autocorrelation 
function for; that will determine which tool to use :)

-Justin

> On Fri, Aug 21, 2009 at 7:57 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> 
>     Jamie Seyed wrote:
> 
>         Hi Mark,
>         Thanks for the information. Actually in 7.4 I found only
>         g_rotacf and
>         g_angle also g_sgangle that calculate rotation and angle correlation
>         function and in appendix D I could not find related topic... I
>         appreciate if
>         someone gives me more detail to do the job.
>         I want to calculate <R(0).R(t)> that R is coordinates vector
>         R(x,y,z) for
>         pure spce water.
> 
> 
>     If that's an auto-correlation function, then g_analyze does the job.
>     Searching for "correlation" in the manual was a good way to start.
>     That would also have found a whole section devoted to the topic,
>     which is good reading.
> 
> 
>         Also I have a question related to having a coordinate file. I
>         did a command
>         as
>         trajconv  -f  md.trr  -n f.ndx  -o md.xtc
>         I am supposing in this case md.xtc contains only x,y,z
>         coordinates. Is that
>         true?? Many Thanks in Advance/Jamie
> 
> 
>     Yes, since the compression algorithm used for .xtc only works on
>     positions. However it is a lossy compression, and if you want
>     full-precision positions-only, look at the options in trjconv -h.
> 
> 
>     Mark
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-- 
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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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