saltpy

A python toolset for calculating and adding salt concentration to solvated atomistic systems

Contents

estimators:

Several methods to estimate the number of ions to add to a solvated solute box.

These include:

• add_neutralize (the add-then-neutralize method)
• genion (gmx genion's version of add-then-neutralize)
• sltcap (as described by Schmit et al., JCTC, 2018)
• split (as described by Machado and Pantano, JCTC, 2020)

calculate

An MDAnalysis driven method for using the estimators on an input solvated structure.

ionize

Wrappers for common MD engines to add ions.

Currently implemented:

• genion (using GromacsWrapper)

Copyright

Copyright (c) 2020, Irfan Alibay

Acknowledgements

Project based on the Computational Molecular Science Python Cookiecutter version 1.3.