Abstract
The GIBS software program is a Grand Canonical Monte Carlo (GCMC) simulation program (written in C++) that can be used for 1) computing the excess chemical potential of ions and the mean activity coefficients of salts in homogeneous electrolyte solutions; and, 2) for computing the distribution of ions around fixed macromolecules such as, nucleic acids and proteins. The solvent can be represented as neutral hard spheres or as a dielectric continuum. The ions are represented as charged hard spheres that can interact via Coulomb, hard-sphere, or Lennard-Jones potentials. In addition to hard-sphere repulsions, the ions can also be made to interact with the solvent hard spheres via short-ranged attractive square-well potentials. In GIBS, the excess chemical potential of ions is computed using the adaptive iterative GCMC algorithm developed by Malasics and Boda (Journal of Chemical Physics, 132, 2010). The standard Metropolis algorithm is used to sample the distribution of ions, which determines the acceptance rates for inserting, deleting, and displacing an ion at each simulation step. The site for inserting an ion is randomly selected based on a cavity-biased, grid-insertion algorithm developed by Woo et al (Journal of Chemical Physics, 121, 2004). GIBS can handle systems of different ion sizes, and implements an efficient algorithm to track the list of cavities available for each particle type(ion and solvent hard spheres) after every single-particle insertion/deletion/displacement, and to quickly sample this list and select the site for inserting a particle. The GIBS program was written by Dr. Dennis G. Thomas in collaboration with Dr. Nathan A. Baker, at Pacific Northwest National Laboratory. The program was developed as part of projects funded by the National Institutes of Health through R01 Grant Nos. GM076121-04S1 and GM099450.
Exploratory License
Eligible for exploratory license
Market Sector
Biological Sciences and Omics