[gmx-users] correlation function

[Justin A. Lemkul]

Jamie Seyed wrote:
> Hi Justin,
> Thanks for the answer. I want to calculate auto-correlation function of 
> R(x,y,z). I mean <R(0).R(t)> , .../Many Thanks in Advance/Jamie
> 

Coordinates?  Use g_traj.

-Justin

> On Sat, Aug 22, 2009 at 6:40 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================