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Published August 3, 2023 | Version v1
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Input files for the MD simulations and free energy calculations for the article "Water Dissolved in a Variety of Polymers Studied by Molecular Dynamics Simulation and a Theory of Solutions"

Description

Article: J. Phys. Chem. B. 125, 9357–9371 (2021) [DOI: 10.1021/acs.jpcb.1c04818]

The structures of the homopolymers and copolymers simulated are shown in Figures 1 and S1 and Tables 2 and 3. All-atom MD simulation was carried out using GROMACS, and this repository provides the input files with the GAFF/RESP force and initial coordinate files. The free energy of water dissolution was obtained with ERmod, and the input files for the free-energy calculations are also contained. See the README files for details.

Notes

This work is supported by the Grant-in-Aid for Scientific Research (No. JP19H04206) from the Japan Society for the Promotion of Science and by the Fugaku Supercomputer Project (No. JPMXP1020200308) and the Elements Strategy Initiative for Catalysts and Batteries (No. JPMXP0112101003) from the Ministry of Education, Culture, Sports, Science, and Technology. The simulations were conducted partly using ITO at Kyushu University, supercomputers at Institute for Solid State Physics of University of Tokyo and at Research Center for Computational Science of National Institutes of Natural Science, OCTOPUS at Osaka University, and Fugaku at RIKEN Advanced Institute for Computational Science through the HPCI System Research Project (Project IDs: hp200065, hp200097, hp200120, hp210140, and hp210176).

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Related works

Is supplement to
Journal article: 10.1021/acs.jpcb.1c04818 (DOI)