  The ionic environment of biomolecules strongly influences their structure,
conformational stability, and inter-molecular interactions.This paper
introduces GIBS, a grand-canonical Monte Carlo (GCMC) simulation program for
computing the thermodynamic properties of ion solutions and their distributions
around biomolecules. This software implements algorithms that automate the
excess chemical potential calculations for a given target salt concentration.
GIBS uses a cavity-bias algorithm to achieve high sampling acceptance rates for
inserting ions and solvent hard spheres in simulating dense ionic systems. In
the current version, ion-ion interactions are described using Coulomb,
hard-sphere, or Lennard-Jones (L-J) potentials; solvent-ion interactions are
described using hard-sphere, L-J and attractive square-well potentials; and,
solvent-solvent interactions are described using hard-sphere repulsions. This
paper and the software package includes examples of using GIBS to compute the
ion excess chemical potentials and mean activity coefficients of sodium
chloride as well as to compute the cylindrical radial distribution functions of
monovalent (Na$^+$, Rb$^+$), divalent (Sr$^{2+}$), and trivalent (CoHex$^{3+}$)
around fixed all-atom models of 25 base-pair nucleic acid duplexes. GIBS is
written in C++ and is freely available community use; it can be downloaded at
https://github.com/Electrostatics/GIBS.
