[gmx-users] correlation function

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 24 01:32:33 CEST 2009

>     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 



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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