No Sir. I am talking about the cosine content of the pca projection (not
dihedral pca), which is also a measure of convergence of the md simulation.
On Tue, Apr 30, 2019 at 6:47 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> By "cosine content" do you mean performing principal component
> analysis in dihedral space instead of Cartesian? If so, then yes
> cpptraj can do this. There's even an example in the manual - see
> 'Dihedral covariance matrix calculation' in the 'Analysis Examples'
> section of the cpptraj part of the Amber manual.
>
> If you want to convert to a Gromacs format, use either the command
> line or 'trajout' and convert to 'trr' or 'xtc' format (see manual for
> details).
>
> -Dan
>
> On Tue, Apr 30, 2019 at 1:23 AM Rajarshi Roy <phd1701171011.iiti.ac.in>
> wrote:
> >
> > Dear AMBER users and Development Team,
> > I have a query on principal component analysis using cpptraj. Does
> cpptraj
> > calculate cosine content of the PC? If so, Can we print that data in a
> > file? Can it be possible in new ambertools? As we know it can be done in
> > gromacs, so which is the best and quick way to convert amber trajectory
> to
> > gromacs trajectory?
> >
> > Thank you in advance.
> >
> > --
> > *with regards*
> >
> > *Rajarshi Roy*
> >
> >
> > *PhD Research Scholar*
> >
> > *Biosciences and Biomedical Engineering*
> >
> > *Indian Institute of Technology, Indore*
> > *India*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
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>
--
*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*India*
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Received on Tue Apr 30 2019 - 09:00:02 PDT
