I'm aware of the corr command, yes.
On Thu, Jul 17, 2014 at 12:56 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> 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,
>
> -Dan
>
>
> On Wed, Jul 16, 2014 at 5:40 PM, Jose Borreguero <borreguero.gmail.com>
> wrote:
>
> > 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
> > 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 17 2014 - 07:00:02 PDT
