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RISMiCal

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

This is a structure analysis program for solutes and solvents, based on the statistical mechanics theory of liquids. The program determines the solvent density distribution surrounding the solute, and calculates various physical values such as the solvation free energy, compressibility, and partial molar volume. The program implements a parallelized fast Fourier transform routine for large-scale parallel computing, and can analyze molecular functions such as the ligand binding affinity of proteins, that would be difficult using other methods.

Information
Last Update:2025/02/10

Official site

https://rismical-dev.github.io/

License

MIT Licence

Availability

Linux, Mac, Ubuntu/Debian for Windows
Core Developers

Norio Yoshida (Graduate School of Informatics, Nagoya University)
Target substance/model

Biopolymers including proteins and DNA, aqueous solutions
Physical quantities that can be computed

Hydration structure, hydration free energy, pseudo dynamics, molecular recognition
Methodology

RISM/3D-RISM
Related keywords
Document

Please cite following papers for your publications including the results obtained by RISMiCal.

  1. Y. Maruyama and N. Yoshida, “RISMiCal: A software package to perform fast RISM/3D-RISM calculations,” J. Comput. Chem., (2024) 45, 1470-1482 (DOI: 10.1002/jcc.27340)
  2. N. Yoshida, “The Reference Interaction Site Model Integrated Calculator (RISMiCal) program package for nano- and biomaterials design,” IOP Conf. Series: Materials Science and Engineerging, 773 (2020),012062 (DOI: 10.1088/1757-899X/773/1/012062)

For GPU code

  1. Y. Maruyama and F. Hirata, “Modified Anderson method for accelerating 3D-RISM calculations using graphics processing unit,” J. Chem. Theory Comput., 8 (2012) 3015-3021 (DOI: 10.1021/ct300355r)

For RISM/3D-RISM-SCF

  1. N. Yoshida and F. Hirata, “A new method to determine electrostatic potential around a macromolecule in solution from molecular wave functions,” J. Comput. Chem., 27, (2006), 453-462, (DOI: 10.1002/jcc.20356)
  2. N. Yoshida, “Efficient implementation of the three-dimensional reference interaction site model method in the fragment molecular orbital method,” J. Chem. Phys., 140, (2014) 214118 (13pages) (DOI: 10.1063/1.4879795)

For placevent

  1. D. Sindhikara, N. Yoshida and F. Hirata, “Placevent: an algorithm for prediction of explicit solvent atom distribution — application to HIV-1 protease and F-ATP synthase,” J. Comput. Chem., 33, (2012) 1536-1543, (DOI: 10.1002/jcc.22984)
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