[gmx-users] correlation function

Jamie Seyed jamie.seyed at gmail.com
Mon Aug 24 20:57:39 CEST 2009

On Sun, Aug 23, 2009 at 7:32 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>    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.
> What did you extract with g_traj?  All the coordinates of all the
> molecules? The command line you gave would be helpful here.  It would seem
> that 1296/216 = 6, therefore (and this is just a guess) then g_analyze is
> trying to calculate some sort of ACF between all coordinates: x-x, y-y, z-z,
> x-y, x-z, y-z.  That way, you'd be getting these ACF's for each individual
> molecule.  Again, just a guess.

Hi Justin,
I think that I extract only the coordinates for my desired atoms using this
g_traj  -f  f.xtc  -s f.tpr  -n f.ndx  -ox coord.xvg
and then
g_analyze  -f coord.xvg  -ac autocorr.xvg

Is that the way to get ACF or I am doing something wrong here?? Many Thanks
in Advance/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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