mond 0.2.4

Monte Carlo Simulation to dissolve a molecule in a mixture of other molecules

monte-solver

Monte Carlo dissolver.

Why

Studying molecules in solution is super interesting.

What

It is a module to automatically prepare sample mixtures for solutions in e.g. gas phase or liquid phase from multiple molecules according to defined concentration

Converting pdb files is not trivial

I guess MS chose their native file format as pdb. What does not work now. It is insane.

• openbabel (not working from package man, or uncompilable)
• Chimera (uninstallable on free systems), now Meta
• rdkit (can't output proper pdb files)
• PDBFixer (can't fix broken rdkit files)
• No idea how MDAnalysis might do it
• openff is not compilable

What could work

• mol files?
• using sdf and https://cactus.nci.nih.gov/translate/
• da muss irgendwo ein Leerzeichen rein und nicht bei 1 anfangen we HETATM ist somehow logisch

Periodic

Muss periodische Boundaries selbst reinmachen

Set up notebook visualization

In your environment run

pip install jupyterlab jupyter_contrib_nbextensions nglview
jupyter-nbextension enable --py --sys-prefix widgetsnbextension and jupyter-nbextension enable nglview --py --sys-prefix

XTB

Dringend installieren um MC-search auf die Moleküle zu machen:

Download and add to path

export PATH=/home/your_home/xtb-dist/bin:$PATH

OpenMM

Installing OpenMM from PyPi is nice to avoid conda, but you need to have numpy<2 installed. In case of errors, you may run:

pip install "numpy<2"