Re: AMBER: Amber9 analyze timecorr manual ambigous

From: David A. Case <>
Date: Thu, 12 Jul 2007 12:55:15 -0700

On Thu, Jul 12, 2007, Nicolas Lux Fawzi wrote:

> 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

Damn. We got the writeup on p. 260 corrected (compared to the Amber 8
manual), but missed the fact that the examples are still wrong: both vec1 and
vec2 are required, even if they are the same. I'll post an erratum; thanks
for reporting this.

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


%A C. Peter
%A X. Daura
%A W.F. vanGunsteren
%T Calculation of NMR-relaxation parameters for flexible molecules from
molecular dynamics simulations
%J J. Biomol. NMR
%V 20
%P 297-310
%D 2001

> 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).

A couple of reviews:

%A A.G. Palmer, III
%T NMR characterization of the dynamics of biomacromolecules
%J Chem. Rev.
%V 104
%P 3623-3640
%D 2004

%A D.A. Case
%T Molecular Dynamics and NMR Spin Relaxation in Proteins
%J Acct. Chem. Res.
%V 35
%P 325-331
%D 2002


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Received on Sun Jul 15 2007 - 06:07:29 PDT
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