[gmx-users] correlation function
Justin A. Lemkul
jalemkul at vt.edu
Sun Aug 23 00:40:48 CEST 2009
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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--
========================================
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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