Hi,
To enable this, I just added the keyword 'magnitude' to the
'vectormath' analysis command to the GitHub version of cpptraj
(6.29.3): https://github.com/Amber-MD/cpptraj
You should just be able to add the command after your rms command, e.g.:
rmsd TTT :1-50.C,CA,N savevectors combined vecsout vecall.dat
vectormath vec1 TTT[TV] magnitude out vecall.magnitude.dat
Note you could also change 'out' to be vecall.dat if you want it all
written to the same file.
Hope this helps,
-Dan
On Wed, Oct 2, 2024 at 7:15 AM Dr. Anselm Horn via AMBER
<amber.ambermd.org> wrote:
>
> Dear Amber experts,
>
> can I calculate and output the length of the translation vector obtained
> from an rmsd command for a trajectory within cpptraj?
>
> The fit command goes like:
> rmsd TTT :1-50.C,CA,N savevectors combined vecsout vecall.dat
>
> And thus, the file vecall.dat contains two sets of vectors, i.e. six
> elements per line plus framenumber. Is there a possibility to write out
> the lengths of those vectors?
>
> (Of course, I can post-process the data, but I'm almost sure that
> cpptraj contains the math-magic to do it itself ... However, I could not
> find it in the manual.)
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
>
>
>
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Received on Wed Oct 02 2024 - 09:00:02 PDT
