Dear Dan,
thanks for that prompt and great support!
Best,
Anselm
Am 02.10.2024 um 17:35 schrieb Daniel Roe:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 04 2024 - 01:00:02 PDT
