[AMBER] autocorr of hydrogen bonds

From: Osman, Roman <roman.osman.mssm.edu>
Date: Mon, 29 Aug 2016 13:05:06 +0000

Hello Amberites,

I was wondering whether anybody has used an autocorrelation of hydrogen bonds.
Here is a cpptraj input that I ran:

# Read in trajectory

trajin mcmrjp_free_nw.dcd

hbond HB out mcmrjp_free_hb.dat :17,252,67,206,159,272,27,32,228,245,262,267,165
,183,34,138,239,290,39,143,207,204,162 series uuseries mcmrjp_free_hb.dat avgout
 mcmrjp_free_avg.dat printatomnum
runanalysis lifetime HB[solutehb] out mcmrjp_free_lifet.dat
autocorr HB[solutehb] out mcmrjp_free_auc.dat lagmax 14500

The surprising thing is that I get in the aucorrelation function negative numbers towards the end of the track.
In my opinion this is not possible since the track is made of 0 and 1, so the autocorrelation cannot be < 0.

In fact if I run with
autocorr HB[solutehb] out mcmrjp_free_auc.dat lagmax 14500 nocovar

The autocorrelations become positive.

Am I doing something wrong?

Thanks for your help.

PS: I can provide the trajectory (large) and the output from the autocorrelation.

Roman Osman
Professor of Structural and Chemical Biology
Mount Sinai School of Medicine
New York, NY 10029
(212) 659-8627

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Received on Mon Aug 29 2016 - 06:30:03 PDT
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