Forked from Jens Vive Kildgaard. https://github.com/JensVK/molecule_adding
Systematic addition of a small molecule to an existing cluster/molecule. It is discussed in detail in this paper:
"Hydration of Atmospheric Molecular Clusters: A New Method for Systematic Configurational Sampling"
Jens Vive Kildgaard, Kurt V. Mikkelsen, Merete Bilde, and Jonas Elm,
J. Phys. Chem. A 2018, 122, 5026−5036
http://doi.org/10.1021/acs.jpca.8b02758
Overall, it's a very nice and convenient tool I hope to play around with more.
python ../molecule_adding.py --fibonacci_points 1 --output dimer --header header.txt --format ".xyz" solute.xyz solvent.xyz
- fibonacci_points is 5 by default, but it was creating a much larger number of isomers than necessary for my test case
- including a header file with number of atoms and a comment line to comply with Cartesian XYZ format helps.
Please cite doi.org/10.1021/acs.jpca.8b02758 if using it for scientific publications.