Avogadro feature development?

Dear Avogadro Developers,
I’m curious if any of these three features are currently under development
in some way?

Specifically the ability to:

  1. generate a solvent box (mentioned as a long term goal on your wiki)
  2. specify boundary conditions: particularly for the Molecular Dynamics
    engine, but also for the minimizer (also mentioned on your wiki)
  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)

Avogadro already has a very powerful and versatile minimizer, these features
just seem (at least to me) like logical steps forward. I’m not sure how much
work would be required to realize them though.

Thanks.

Daniel Seeman
PhD Candidate
Chemistry Department
University of Massachusetts, Amherst

  1. generate a solvent box (mentioned as a long term goal on your wiki)

There’s a Packmol plugin:

  1. 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.

  1. 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: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/