Great! Thanks for the info.
-Jose
On Thu, Jan 9, 2014 at 5:55 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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,
>
> -Dan
>
> 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 <borreguero.gmail.com
> >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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jan 09 2014 - 17:00:08 PST
