Re: [AMBER] Utility to compute the auto-correlation function for a dihedral angle?

From: Daniel Roe <>
Date: Thu, 9 Jan 2014 15:55:41 -0700


You can calculate the auto-correlation function of a data set (or
cross-correlation of 2 data sets) in cpptraj with the 'corr' command. Note
however that 'corr' doesn't yet handle periodic data sets properly, so if
your dihedral data 'jumps' (e.g. crosses back and forth from < 180 to >
-180) the result won't be correct. If your data does jump around like this
you can try shifting it by using the the 'range360' argument of the
'dihedral' command prior to calculating the auto-correlation function. If
your data doesn't jump the calculated correlation function should be fine.
The upcoming AmberTools 14 version of cpptraj will correctly calculate
correlation functions for periodic data.

Hope this helps,


PS - Note that by default cpptraj 'corr' really calculates covariance
(which is usually what you want) - to do a raw correlation you need to
specify 'nocovar'.

On Thu, Jan 9, 2014 at 1:02 PM, Jose Borreguero <>wrote:

> Dear Amber gurus,
> I have used ptraj to output the trajectory of a particular dihedral angle
> but it seems there's no utility in ptraj to calculate the autocorrelation
> function. Am I missing something? Otherwise, is there a package or program
> I can use straight away (I'm trying to save me some scripting time) ?
> Thanks in advance!
> -Jose
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jan 09 2014 - 15:00:03 PST
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