TY - JOUR A1 - Bänsch, Felix A1 - Daniel, Mirco A1 - Lanig, Harald A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - An automated calculation pipeline for differential pair interaction energies with molecular force fields using the Tinker Molecular Modeling Package JF - Journal of Cheminformatics N2 - An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. KW - Intermolecular interaction KW - Nonbonding interaction KW - Molecular Force Field KW - Molecular modeling KW - Molecular Dynamics Y1 - 2024 U6 - https://doi.org/10.1186/s13321-024-00890-5 VL - 16 (2024) IS - Artikel Nr. 96 ER - TY - CHAP A1 - Zielesny, Achim A1 - Daniel, Mirco A1 - Lanig, Harald A1 - Steinbeck, Christoph T1 - An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package T2 - 36th Molecular Modeling Workshop, Erlangen, Germany N2 - An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer-monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory-Huggins parameters and isotropic particle-particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLSAA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. Y1 - 2024 N1 - Poster Session, Abstract und Poster im Tagungsband veröffentlicht. ER - TY - CHAP A1 - Bänsch, Felix A1 - Daniel, Mirco A1 - Lanig, Harald A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - A Calculation Pipeline for Differential Molecule Pair Interaction Energies T2 - 35th Molecular Modeling Workshop Y1 - 2023 N1 - Poster Session, Abstract im Tagungsband veröffentlicht. ER - TY - JOUR A1 - van den Broek, Karina A1 - Daniel, Mirco A1 - Epple, Matthias A1 - Schaub, Jonas A1 - Kuhn, Hubert A1 - Zielesny, Achim T1 - PSMILES – A particle-based Molecular Structure Representation for Mesoscopic Simulation JF - Konferenz: 11th International Conference on Chemical Structures, 27.-31. Mai 2018 in Noordwijkerhout, Niederlande Y1 - 2018 UR - http://www.int-conf-chem-structures.org/fileadmin/user_upload/ICCS_2018/posters/P76-Zielesny.pdf ER - TY - JOUR A1 - van den Broek, Karina A1 - Daniel, Mirco A1 - Epple, Matthias A1 - Hein, Jan-Mathis A1 - Kuhn, Hubert A1 - Neumann, Stefan A1 - Truszkowski, Andreas A1 - Zielesny, Achim T1 - MFsim — an open Java all-in-one rich-client simulation environment for mesoscopic simulation JF - Journal of Cheminformatics Y1 - 2020 U6 - https://doi.org/10.1186/s13321-020-00432-9 SN - 1758-2946 VL - 12 SP - 29 ER - TY - JOUR A1 - Truszkowski, Andreas A1 - Daniel, Mirco A1 - Kuhn, Hubert A1 - Neumann, Stefan A1 - Steinbeck, Christoph A1 - Zielesny, Achim A1 - Epple, Matthias T1 - A molecular fragment cheminformatics roadmap for mesoscopic simulation JF - Journal of Cheminformatics Y1 - 2014 U6 - https://doi.org/10.1186/s13321-014-0045-3 SN - 1758-2946 VL - 6 IS - Artikelnr. 45 ER - TY - CHAP A1 - van den Broek, Karina A1 - Daniel, Mirco A1 - Epple, Matthias A1 - Schaub, Jonas A1 - Kuhn, Hubert A1 - Zielesny, Achim T1 - PSMILES – A particle-based Molecular Structure Representation for Mesoscopic Simulation T2 - Konferenz: 11th International Conference on Chemical Structures, 27.-31. Mai 2018 in Noordwijkerhout (Niederlande) Y1 - 2018 ER - TY - JOUR A1 - van den Broek, Karina A1 - Daniel, Mirco A1 - Epple, Matthias A1 - Kuhn, Hubert A1 - Schaub, Jonas A1 - Zielesny, Achim T1 - SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation JF - Journal of Cheminformatics Y1 - 2018 U6 - https://doi.org/10.1186/s13321-018-0294-7 SN - 1758-2946 IS - 10 SP - 35 ER - TY - INPR A1 - Bänsch, Felix A1 - Daniel, Mirco A1 - Lanig, Harald A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package N2 - An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer-monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory-Huggins parameters and isotropic particle-particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. KW - intermolecular interaction KW - molecular force field KW - Flory-Huggins parameter KW - DPD, Dissipative Particle Dynamics Y1 - 2024 U6 - https://doi.org/10.26434/chemrxiv-2024-pkmxm ER - TY - CHAP A1 - Bänsch, Felix A1 - Daniel, Mirco A1 - Lanig, Harald A1 - Steinbeck, Christoph A1 - Zielesny, Achim T1 - A new Approach to DPD Repulsion Parameter Estimation T2 - Konferenz: 34th Molecular Modelling Workshop 2020, 17.-19. Februar 2020 in Erlangen Y1 - 2020 ER -