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sharc-md / sharc

The SHARC molecular dynamics (MD) program suite is an ab initio MD software package developed to study the excited-state dynamics of molecules.
https://www.sharc-md.org
GNU General Public License v3.0
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align.sh #31

Closed ziechys closed 1 year ago

ziechys commented 2 years ago

Hi everyone,

In trajana_nma.py, the script align.sh is mentioned:

https://github.com/sharc-md/sharc/blob/beca9d1d307d1594c0ca7618ca2f5bd85af4eb12/bin/trajana_nma.py#L32

Where can I find this?

Best Michael

maisebastian commented 2 years ago

Dear Michael, if you did calculations in vacuum and your initial conditions do not have translation/rotation momentum (wigner.py removes them by default), then alignment is probably not necessary, and you can simply use the output.xyz files. If you performed QM/MM simulations, then you can use MD tools like VMD to align the chromophore between time steps and write a new xyz file that only contains the chromophore. You can also write an email to our support email address, then I can send you a Python script for this kind of functionality. There is no align.sh script that I am aware of.

Best, Sebastian

felixplasser commented 2 years ago

This is a legacy of the original implementation. I think we can remove this comment in the code.