[gmx-users] correlation function
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.
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
g_analyze -f coord.xvg -ac autocorr.xvg
Is that the way to get ACF or I am doing something wrong here?? Many Thanks
> 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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