GMXPolymer: a generated polymerization algorithm based on GROMACS

• Published in: Journal of molecular modeling Vol. 30; no. 9; p. 320
• Main Authors: Liu, Jianchuan, Lin, Haiyan, Li, Xun
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.09.2024; Springer Nature B.V
• Subjects: Addition polymerization; Algorithms; Amorphous structure; Characterization and Evaluation of Materials; Chemical bonds; Chemistry; Chemistry and Materials Science; Computer Appl. in Life Sciences; Computer Applications in Chemistry; energy; Molecular dynamics; Molecular Medicine; Original Paper; Polymerization; Polymers; Structural reliability; Theoretical and Computational Chemistry; Thermal simulation; Thermodynamic properties; MD simulation; Polymerization; Polymer; GROMACS; Bonds
• ISSN: 1610-2940; 0948-5023; 0948-5023
• DOI: 10.1007/s00894-024-06119-4

Context This work introduces a method for generating generalized structures of amorphous polymers using simulated polymerization and molecular dynamics equilibration, with a particular focus on amorphous polymers. The techniques and algorithms used in this method are described in the main text, and example input scripts are provided for the GMXPolymer code, which is based on the GROMACS molecular dynamics package. To demonstrate the efficacy of our method, we apply it to different glassy polymers exhibiting varying degrees of functionality, polarity, and rigidity. The reliability of the method is validated by comparing simulation results with experimental data in various structural and thermal properties, both of which show excellent agreement. Methods This work implements the GMXPolymer simulated polymerization algorithm on the GROMACS program. GMXPolymer code controls the main polymerization loop. The energy minimizations and molecular dynamics simulations use the GROMACS program called by the GMXPolymer code. A new ITP file is generated when a new bond is formed, and the necessary additions to the ITP file are made to include new bonds, angles, and dihedrals. In preparing the ITP file of the monomer, the charge of the reactive atom must be modified before the code runs so that it is a correct value after bonding.