Ermod: Fast and versatile computation software for solvation free energy with approximate theory of solutions |
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| Authors: | Shun Sakuraba Nobuyuki Matubayasi |
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| Affiliation: | 1. Quantum Beam Science Directorate, Japan Atomic Energy Agency, Kizugawa, Kyoto, Japan;2. Institute for Molecular Science, Okazaki, Aichi, Japan;3. Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka, Japan;4. Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto, Japan;5. Japan Science and Technology Agency (JST), CREST, Kawaguchi, Saitama, Japan |
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| Abstract: | ERmod is a software package to efficiently and approximately compute the solvation free energy using the method of energy representation. Molecular simulation is to be conducted at two condensed‐phase systems of the solution of interest and the reference solvent with test‐particle insertion of the solute. The subprogram ermod in ERmod then provides a set of energy distribution functions from the simulation trajectories, and another subprogram slvfe determines the solvation free energy from the distribution functions through an approximate functional. This article describes the design and implementation of ERmod, and illustrates its performance in solvent water for two organic solutes and two protein solutes. Actually, the free‐energy computation with ERmod is not restricted to the solvation in homogeneous medium such as fluid and polymer and can treat the binding into weakly ordered system with nano‐inhomogeneity such as micelle and lipid membrane. ERmod is available on web at http://sourceforge.net/projects/ermod . © 2014 Wiley Periodicals, Inc. |
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| Keywords: | solvation free energy energy representation solution theory molecular simulation distribution function |
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