GIBS: A grand-canonical Monte Carlo simulation program for simulating ion-biomolecule interactions

TL;DR

GIBS is a new grand-canonical Monte Carlo simulation software designed to accurately model ion distributions and thermodynamic properties around biomolecules, aiding understanding of ionic effects in biological systems.

Contribution

The paper introduces GIBS, a novel GCMC simulation program with advanced algorithms for ion and solvent sampling, specifically tailored for dense ionic biomolecular environments.

Findings

Successfully computed ion excess chemical potentials for NaCl.

Generated radial distribution functions for various ions around nucleic acids.

Demonstrated high sampling efficiency with cavity-bias algorithm.

Abstract

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.