These files are for simulating Grotthuss diffusion of protons in water, as described in
"Grotthuss Molecular Dynamics Simulations for Modeling Proton Hopping in Electrosprayed Water Droplets" L. Konermann and S. Kim, J. Chem. Theory Comput. 18, 3781–3794 (2022)
https://pubs.acs.org/doi/10.1021/acs.jctc.2c00001
PLEASE CITE THIS PAPER WHEN USING ANY OF THE FILES IN THIS REPOSITORY. THANK YOU.
Simulations are performed by alternating between brief Gromacs run segments (using static protons), and a Python program (which performs proton hopping).
There are two directories, each with its own README file
- In /H3O_H2O_droplet_Grotthuss we perform Grotthuss diffusion on an existing droplet with 3 H3O+ (quite simple).
- In /H3O_H2O_droplet_make_evap_Grotthuss we generate a droplet, equilibrate, and perform Grotthuss diffusion with occasional removal of evaporated molecules (a bit more complicated).
Questions? Lars Konermann, konerman@uwo.ca