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ERmod

  • Openness:3 ★★★
  • Document quality:2 ★★☆

ERmod is software for calculating the free energy in soft, molecular aggregate. This program rapidly and accurately calculates the free energy of binding of a molecule in the aggregate through combination of the molecular dynamics simulation and the energy-representation theory of solvation. The solubility of a molecule can be determined with ERmod in arbitrary solvent including supercritical fluid and ionic liquid. Assessment is also possible for the binding strength and site of a molecule in micelle, lipid membrane or protein.

Information
Last Update:2021/03/06

Official site

https://sourceforge.net/projects/ermod/

License

GPL v2
Availability Normal PC clusters, K supercomputer, and other regional supercomputers. Installation on Kobe FOCUS currently in progress (as of April 25, 2015). Refer to the following guides for installation instruction on various environments: https://sourceforge.net/p/ermod/wiki/build-Guide/ https://sourceforge.net/p/ermod/wiki/build-Supercom/
Core Developers Nobuyuki Matsubayashi（Graduate School of Engineering Science, Osaka University）、Shun Sakuraba（Japan Atomic Energy Agency）
Target substance/model Solutions (including non-aqueous, ionic fluids, and supercritical fluids), lipid membranes, micelles, polymers, and QM/MM systems
Physical quantities that can be computed Free energy; energy distribution function
Methodology Calculation and analysis of the free energy of solution systems and nanoscale heterogeneous weakly ordered systems using energy representation method
Parallelization Parallel computing by MPI and OpenMP is supported (OpenMP parallel computing needs an option).
Related keywords
Document https://sourceforge.net/p/ermod/wiki/doc-Theories/
Other

The application’s greatest appeal

Software for calculating the free energy of molecular aggregate systems. Combines molecular dynamics and the theory of solutions in the energy representation method, enabling rapid, high-precision calculation of the free energy of substances binding to molecular aggregates. The software supports normal solutions, and it can also determine the solubility of a wide range of solvent species such as supercritical fluids and ionic fluids. Bonding strengths and sites for materials bonding to micelles, lipid membranes, and proteins can also be evaluated.
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