AMBER Archive (2007)

Subject: AMBER: Amber9 analyze timecorr manual ambigous

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Thu Jul 12 2007 - 14:26:19 CDT

Hello

I had a few questions:
1. I was slightly confused by the amber9 manual ptraj section pg 260
where it says referring to vec1 and vec2 vecnames:

"if the two vectors are the same, the result is an autocorrelation function"

while it seems clear from the example on pg 261 that you only need to
specify vec1 to get an autocorrelation function:

analyze timecorr vec1 v0 tstep 1.0 tcorr 100.0 out v0.out

maybe the manual should be updated to reflect that, since the string of
arguments for analyze timecorr makes it seem like vec2 needs to be specified

2. Can you give me more detail on the difference between drct direct
approach and FFT method?

3. If it's not too much trouble, can you point me to some literature
references using this functionality, specifically the dplr keyword (I'm
trying to compute some timecorrelation functions for NMR dynamics
comparisons).

Thanks for your help.

-Nick

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