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
run
runanalysis lifetime HB[solutehb] out mcmrjp_free_lifet.dat
autocorr HB[solutehb] out mcmrjp_free_auc.dat lagmax 14500
run
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
roman.osman.mssm.edu<mailto:roman.osman.mssm.edu>
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Received on Mon Aug 29 2016 - 06:30:03 PDT
