GIBS: Grand Canonical Monte Carlo (GCMC) simulation program for computing ion distributions around biomolecules with hard sphere solvent models

GIBS is a Grand canonical Monte Carlo (GCMC) simulation program for computing the thermodynamic properties of ionic solutions and their distributions around biomolecules. GIBS 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 when simulating dense ionic systems. In the current version, ion-ion interactions can be described using Coulomb, hard-sphere, or Lennard-Jones (L-J) potentials; solvent-ion interactions can be described using hard-sphere, L-J and attractive square-well potentials; and, solvent-solvent interactions are described using hard-sphere repulsions. GIBS can be used as a platform to evaluate new implicit solvent and coarse-grained models for predicting the thermodynamics properties of ionic solutions. GIBS is written in C++ and is available freely for the community to use as an educational and as a research tool.

The GIBS program was written by Dr. Dennis G. Thomas in collaboration with Dr. Nathan A. Baker, at the 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.

Main Features

1. Automated excess chemical potential calculations for bulk electrolyte solutions.
2. Fast and efficient GCMC sampling of ion distributions in bulk electrolyte solutions and around fixed molecular solutes.
3. Models for Ion-Ion interactions using Coulomb, hard-sphere, Lennard-Jones potentials.
4. Models for Ion-Solvent interactions using hard-sphere, Lennard-Jones, attractive square well potentials.
5. Models for Solvent-Solvent interactions using hard-sphere repulsions.
6. Solvent representation as dielectric continuum (primitive model) or as hard spheres (solvent primitive model or SPM).
7. Ion representation as charged hard spheres.

Current Version

The current version is version 1

Citing GIBS

A publication has been planned.

Disclaimer

This material was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor the United States Department of Energy, nor Battelle, nor any of their employees, nor any jurisdiction or organization that has cooperated in the development of these materials, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness or any information, apparatus, product, software, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof, or Battelle Memorial Institute. The views and opinions of authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof.

PACIFIC NORTHWEST NATIONAL LABORATORY operated by BATTELLE for the UNITED STATES DEPARTMENT OF ENERGY under Contract DE-AC05-76RL01830