Ghostly is a package to perform modification of ghost (dummy) atom bonded terms for alchemical free-energy calculations, using the approach described in the paper "Dummy Atoms in Alchemical Free Energy Calculations" by Fleck et al., JCTC, 2021, 17, 7, 4403-4419. These modifications were designed to solve two key issues:

To ensure that ghost atoms only give a multiplicative contribution to the partition function, which will cancel when computing double free-energy differences.
To avoid spurious coupling between the physical and ghost systems, which can affect the equilibrium geometry of the physical system.

To install:

conda install -c conda-forge -c openbiosim ghostly

To install the development version:

conda install -c conda-forge -c openbiosim/label/dev ghostly

When updating the development version it is generally advised to update Sire at the same time:

conda install -c conda-forge -c openbiosim/label/dev ghostly sire

Filters