The signac project used to run and manage the molecular dynamics simulations for https://doi.org/10.1021/acs.jpcc.0c05311.
- GAFF Force field for acetonitrile, chloroform, and TFSI- anion
- Amber Force field for Li+ ion
- Acetonitrile, chloroform, and TFSI- partial charges calculated through RESP using Gaussian09 and the R.E.D Server
- Li+ and TFSI- partial charges scaled by 0.8
- Simulations run with GROMACS 2018.5
The signac project can be initialized by running python src/init.py on the command line. This command initializes the project and creates all of the necessary signac jobs. Various commands can be executed by running python src/project.py [command].
All data managed by signac can be impored to a csv file by running: python dataframe.py. All plotting functions are contained within plot_pandas.py.
The list of packages and dependencies can be viewed and installed via the environment.yml file.
The R.E.D Server was used to derive the partial charges for the acetonitrile, chloroform, and TFSI-. To reproduce this work, start by going to the R.E.D Server here and clicking the submit button at the top right. Once the pop-up appears, click on the private account link at the bottom to submit a job to the server using your account (Create one if you haven't done so already). The program Gaussian09E.01 was used for this work. The tarballs for the different molecules are contained withing the red_server directory as well as the uncompressed folders.