ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules |
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| Authors: | Andreas Vitalis J. Andrew McCammon? |
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| Affiliation: | 1. Department of Chemistry and Biochemistry , University of California at San Diego , Gilman Dr., Mail Code, 92093-0365, San Diego, CA, USA;2. Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, Department of Pharmacology , University of California at San Diego.Gilman Dr. , Mail Code, 92093-0365, San Diego, CA, USA |
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| Abstract: | In this work we present a new software package (ISIM), which represents a flexible, computational tool for simulations of electrolyte solutions via a grand canonical Monte Carlo procedure (GCMC) with a specific capability of treating biomolecules in solution. The GCMC method provides a powerful tool for studying the ionic environments of highly charged macromolecules with attention to the atomic detail of both the solute and the mobile counterions. The ISIM software differs from previous schemes mainly by treating different ion types independently and offering a new parameterization procedure for calibrating excess chemical potentials and bulk ion concentrations. Additionally, ISIM leverages the APBS software package to provide accurate descriptions of the biomolecular electrostatic potential through the efficient solution of Poisson's equation. ISIM has been validated on a variety of test systems; we successfully reproduce elementary properties of electrolyte solutions as well as theoretical and experimental results for challenging test systems like Calmodulin and DNA. |
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| Keywords: | Grand canonical Monte Carlo Ion simulation ISIM software Electrostatics |
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