The purpose of saltswap to allow users to specify the macroscopic salt concentration of the reservoir that their simulation will be coupled to. However, the driver for saltswap (swapper) requires the specification of the chemical potential, not the salt concentration. This PR is for a wrapper, called Salinator, that uses calibration data to convert the specified salt concentration to the required chemical potential.
This wrapper also addresses issue #11, which is how to include neutralizing counter-ions. This wrapper also implements the solution discussed in #11: neutralizing the system with ions that have the same topology as the water model. The same functions also make it easy to initialize the number of salt pairs in the system.
The purpose of
saltswapto allow users to specify the macroscopic salt concentration of the reservoir that their simulation will be coupled to. However, the driver for saltswap (swapper) requires the specification of the chemical potential, not the salt concentration. This PR is for a wrapper, calledSalinator, that uses calibration data to convert the specified salt concentration to the required chemical potential.This wrapper also addresses issue #11, which is how to include neutralizing counter-ions. This wrapper also implements the solution discussed in #11: neutralizing the system with ions that have the same topology as the water model. The same functions also make it easy to initialize the number of salt pairs in the system.