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*
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Received on Tue Apr 30 2019 - 06:30:03 PDT
