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Free_energy_calculation_textbook_in_English.pdf
(289846 bytes)
MolecularTheory_of_Solvation_Text_in_Japanese.pdf
(207043 bytes)
Theoretical Details
ERmod calculates approximate solvation free energy based on the energy representation method (in some references this is paraphrased as energetic representation method).
There are some reviews about the computation of solvation free energy in computer simulation:
- Theories to compute solvation free energy (English)
- Theories to compute solvation free energy (Japanese)
Primary citations for the energy representation method are:
- General formulation: N. Matubayasi and M. Nakahara, J. Chem. Phys. 113, 6070-6081 (2000).
- Approximate functional for the solvation free energy: N. Matubayasi and M. Nakahara, J. Chem. Phys. 117, 3605-3616 (2002); erratum, J. Chem. Phys. 118, 2446 (2003).
- Remarks about intramolecular flexibility: N. Matubayasi and M. Nakahara, J. Chem. Phys. 119, 9686-9702 (2003).
- General design of ERmod software and technical notes: S. Sakuraba and N. Matubayasi, J. Comput. Chem. 35, 1592–1608 (2014). Footnote 1 on page 1598 of this paper is incorrectly stated. The TIP3P model used for the calculations was the CHARMM-modified one with a Lennard-Jones term on the hydrogen atom.
Extension and representative applications are:
- Application to micelle: N. Matubayasi, K. K. Liang, and M. Nakahara, J. Chem. Phys. 124, 154908 (13 pages) (2006).
- Application to lipid membrane: N. Matubayasi, W. Shinoda, and M. Nakahara, J. Chem. Phys. 128, 195107 (13 pages) (2008).
- Application to solid-liquid interface: N. Yamamoto, I. Nakakuki, and N. Matubayasi, J. Chem. Phys. 149, 014504 (10 pages) (2018).
- All-atom calculation of free energy of protein solvation: Y. Karino and N. Matubayasi, J. Chem. Phys. 134, 041105 (4 pages) (2011).
- Application to polymer: T. Kawakami, I. Shigemoto, and N. Matubayasi, J. Chem. Phys. 137, 234903 (9 pages) (2012).
- Test against existing methods: Y. Karino, M. V. Fedorov, and N. Matubayasi, Chem. Phys. Lett. 496, 351-355 (2010).
- Combination with QM/MM method: H. Takahashi, N. Matubayasi, M. Nakahara, and T. Nitta, J. Chem. Phys. 121, 3989-3999 (2004).
- Application to reduction potential (free energy of electron attachment): H. Takahashi, H. Ohno, R. Kishi, M. Nakano, and N. Matubayasi, J. Chem. Phys. 121, 205103 (14 pages) (2008).
