[CP2K:2027] visual approach to construction of QMMM input

Teodoro Laino teodor... at gmail.com
Tue Apr 21 14:55:12 UTC 2009

Hi Peter,

thanks for posting this useful info!
I'm pretty sure this will be definitely useful.

I have a feature request! :-p

Im not an expert of pymol, but do you think would it be easily feasible 
to have a full applet (with input field structure parsed from an 
up-2-date xml cp2k input tree) in order to allow the creation of the 
whole CP2K input graphically?
This, combined with the graphical handling of the molecular system, may 
be really an interesting feature.

I'm ready to bet that this would have even more appeal ;-)

Peter wrote:
> Dear CP2K users,
> Recently I've written a simple script, which could be helpful to those
> of us, who deals with large QMMM systems.
> The script is intended to be used from PyMol (http://www.pymol.org/)
> molecular visualization system and allows one to generate &QM_KIND,
> &LINK and &CELL parts of CP2K input easily. Given a molecular object
> name and QM part selection name (which can be defined using either
> approach available in PyMol) it generates output file with
> corresponding input groups.
> To use the script:
>   1. Download it (http://groups.google.com/group/cp2k/web/gen-cp2k-
> qmmm.py)
>   2. Start PyMol and issue the following command from it's shell:
>      >  run /path/to/script.py
>   3. Use it:
>     > gen_cp2k_qmmm filename, qm_part_selection_name,
> the_whole_system_object
> The output will be saved to file "filename".
> N.B.: The file will be overwritten!
> Another PyMol script which you may find handy is a multiframe XYZ file
> (trajectory) loader (http://groups.google.com/group/cp2k/web/
> load_xyz_traj.py).
> "Installation procedure" is pretty the same.
> Usage:
>  > load_xyz_traj file.xyz, target_object [, stride]
> N.B.: By default PyMol reorders atoms on molecule load. This PyMol
> behavior may prevent correct loading of XYZ trajectories. To
> workaround this issue add the following lines to ~/.pymolrc file
> (create it if needed):
> set retain_order, 1
> set pdb_retain_ids, 1
> Hopefully these simple scripts will help people familiar with PyMol in
> doing biostuff with CP2K.
> Best regards,
> Peter
> >

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