mlund / si-thiocyanate

A Molecular Forcefield for Thiocyanate Anions in Water and at Interfaces

A Molecular Forcefield for Thiocyanate Anions in Water and at Interfaces

This repository contains Jupyter Notebooks and simulation data for reproducing the work of the scientific paper Specific Cation Effects on SCN^- in Bulk Solution and at the Air–Water Interface, DOI: 10.1021/acs.jpcb.8b02303.

Layout

• notebook.ipynb Jupyter Notebook to analyze all simulation data and generate plots
• notebook.html Jupyter Notebook in HTML format
• simulations/openmm/OpenMM.ipynb Jupyter Notebook to perform MD simulations of bulk salt solutions using OpenMM
• simulations/gmx/ All GROMACS files needed to perform MD simulations of air–salt solution interfaces
• dft/ Jupyter Notebook to perform quantum-chemical calculations using MOLCAS
• bulk/ OpenMM and GROMACS MD simulation data on aqueous salt solutions and Kirkwood-Buff analysis
• interface/ Gromacs MD simulation data on air–salt solution interfaces and surface tension analysis

Usage

To open the Notebooks, install python via Miniconda and make sure all required packages are loaded by issuing the following terminal commands

    conda env create -f environment.yml
    source activate thiocyanate
    jupyter-notebook