> 1) generate a solvent box (mentioned as a long term goal on your wiki)
There's a Packmol plugin:
https://github.com/timvdm/Avogadro-Packmol-Extension
> 2) specify boundary conditions: particularly for the Molecular Dynamics
> engine, but also for the minimizer (also mentioned on your wiki)
I don't currently know anyone working on this -- the MM and MD code all lives
in Open Babel. A quick-and-dirty approach probably wouldn't take too long,
although handling bonds across the unit cell might be tricky.
> 3) incrementally save out a file (say a sequentially numbered series of pdb
> files) after x number of minimization steps (obviously this can be done
> manually, but it would be nice if there were a way to automate it)
No one is working on that, but it wouldn't be too difficult. You'd want to
modify the Avogadro force field extension to do that -- add an option to
specify the filename and X steps.
In either case #2 or #3, either myself or someone else can point you to
specific parts of the code if that helps.
Hope that helps,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: [email protected]
web: http://hutchison.chem.pitt.edu/
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