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.