Re: [AMBER] How do I apply cpptraj.timecorr to the output dataset of cpptraj.dihedral?

From: Daniel Roe <>
Date: Wed, 16 Jul 2014 22:56:39 -0600


Be aware that timecorr converts the vector Cartesian XYZ coordinates into
spherical harmonics, which is most useful in the context of comparing to
NMR data. If you just want the straight up autocorrelation (or cross
correlation) just use the 'corr' command, which is able to handle periodic
data sets. Be aware that the data must be generated with a cpptraj Action
(e.g. dihedral, pucker, etc) for cpptraj to know it is periodic (i.e. sets
read with readdata won't be periodic).

Hope this helps,


On Wed, Jul 16, 2014 at 5:40 PM, Jose Borreguero <>

> Dear Amber users,
> I want to calculate the time autocorrelation function of a dihedral angle.
> I've used dihedral command from cpptraj to get the angle. For instance:
> dihedral theta .Si6 .C18 .C20 .C24 out theta.dat
> Command timecorr requires a vector as input, so I guess my question is how
> do I translate dataset theta into vector set (cos(theta), sin(theta), 0) so
> that I can feed it to timecorr.
> Related question: with output file theta.dat I can create file vector.dat
> with columns cos(theta), sin(theta), and 0. Then is it possible to read
> file vector.dat into a vector set that I can pass to timecorr?
> Best regards,
> -Jose Borreguero
> _______________________________________________
> 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 Wed Jul 16 2014 - 22:00:03 PDT
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