Workflow ideas for 2018 Avogadro UGM

workflow-ideas.md

Avogadro

• get / modify selection (e.g., enlarge by x Å)
• create enantiomer
• “Random alloy” - Replace x% atom X -> atom Y

Scikit-nano https://docs.scikit-nano.org

• MWNT
• Graphene or TMDC multilayers?

Pymatgen https://github.com/materialsproject/pymatgen

• create a slab
• nanoparticle with Wulff

STK https://lukasturcani.github.io/stk/docs/build/html/

• polymers
• cages
• COF
  • hexagonal, honeycomb, kagome, square

RDKit http://www.rdkit.org/docs/GettingStartedInPython.html

• get ETKDG conformer

ASE

• Generate MoS2 https://wiki.fysik.dtu.dk/ase/ase/build/surface.html#ase.build.mx2
• Generate TIP water box: https://wiki.fysik.dtu.dk/ase/tutorials/tipnp_equil/tipnp_equil.html

GenIce - https://github.com/vitroid/GenIce/

• Generate ice unit cell

PackMol https://github.com/choderalab/openmoltools/blob/master/openmoltools/packmol.py

• Pack current molecule http://timvdm.blogspot.com/2010/03/avogadros-packmol-plugin.html

Glycam(?)

• Sugar / oligosaccaride builder?