1. Rühle, C. Junghans, A. Lukyanov, K. Kremer, and D. Andrienko, Versatile Object-oriented Toolkit for Coarse-graining Applications, J. Chem. Theor. Comp., 2009, 5(12):3211-3223,

    1. Lyubartsev, and A. Laaksonen, Calculation Of Effective Interaction Potentials From Radial-Distribution Functions - A Reverse Monte-Carlo Approach, Phys. Rev. E, 52(4):3730–3737, 1995,

  1. Tschöp, K. Kremer, J. Batoulis, T. Burger, and O. Hahn, Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates, Acta Polymerica, 49:61–74, 1998,;2-V

  1. Reith, M. Pütz, and F. Müller-Plathe, Deriving effective mesoscale potentials from atomistic simulations, J. Comp. Chem., 24(13):1624–1636, 2003,

  1. Izvekov, and G. A. Voth, Multiscale coarse graining of liquid-state systems, J. Chem. Phys., 123(13):134105, 2005,

    1. Noid, J. Chu, G. S. Ayton, V. Krishna, S. Izvekov, G. A. Voth, A. Das, and H. C. Andersen, The multiscale coarse graining method. 1. A rigorous bridge between atomistic and coarse-grained models, J. Chem. Phys., 128:244114, 2008,

  1. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl. Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation., J. Chem. Theo. Comp., 4(3):435–447, 2008,

  1. Murtola, E. Falck, M. Karttunen, and I. Vattulainen, Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints, J. Chem. Phys., 126(7):075101, 2007,

  1. Wang, C. Junghans, and K. Kremer, Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?, Eur. Phys. J. E, 28(2):221–229, 2009,

  1. Fritz, V. A. Harmandaris, K. Kremer, and N. F. A. van der Vegt, Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities, Macromolecules, 42(19):7579-7588, 2009,

  1. Ganguly, D. and Mukherji, C. Junghans, and N. F. A. van der Vegt, Kirkwood-Buff coarse-grained force fields for aqueous solutions, J. Chem. Theor. Comp., 8(5):1802-1807, 2012,

  1. Rühle, and C. Junghans, Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane, Macromolecular Theory and Simulations, 20(7):472–477, 2011,

    1. Mashayak, M. N. Jochum, K. Koschke, N. R. Aluru, V. Rühle, and C. Junghans, Relative entropy and optimization-driven coarse-graining methods in VOTCA, Plos One, 10(7):e131754, 2015,

    1. Shell, The relative entropy is fundamental to multiscale and inverse thermodynamic problems., J. Chem. Phys., 129:144108, 2008,

  1. Wu, and D. A. Kofke, Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation., J. Chem. Phys., 123:054103, 2005,

    1. Rudzinski, and W. G. Noid, Coarse-graining entropy, forces, and structures, J. Chem. Phys., 135:214101, 2011,

  1. Chaimovich, and M. S. Shell, Coarse-graining errors and numerical optimization using a relative entropy framework, J. Chem. Phys., 134:094112, 2011,

  1. Lyubartsev, A. Mirzoev, L.J. Chen, and A. Laaksonen, Systematic coarse-graining of molecular models by the Newton inversion method, Faraday discussions, 144:43–56, 2010,

  1. Lu, Y. and Qiu, R. Baron, and V. Molinero, Coarse-Graining of {TIP}4P/2005, {TIP}4P-Ew, {SPC}/E, and {TIP}3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization, J. Chem. Theor. Comp., 10:4104–4120, 2014,

    1. de Oliveira, P. A. Netz, K. Kremer, C. Junghans, and D. Mukherji, C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids, J. Chem. Phys., 144:174106, 2016,

  1. Rosenberger, M. Hanke, N. F. A. van der Vegt, Comparison of iterative inverse coarse-graining methods, Eur. Phys. J. Special Topics 225, 1323-1345, 2016,

    1. Kirkwood, and F. P. Buff, The Statistical Mechanical Theory of Solutions. I, J. Chem. Phys., 19(6):774–777, 1951,

  1. Delbary, M. Hanke and D. Ivanizki, A generalized Newton iteration for computing the solution of the inverse Henderson problem, Inverse Probl. Sci. Eng., 28(8):1166-1190 2020,

    1. Bernhardt, M. Hanke and N. F. A. van der Vegt, Iterative integral equation methods for structural coarse-graining, J. Chem. Phys., 154:084118, 2021,

    1. Thompson, H. M. Aktulga, R. Berger, D. S. Bolintineanu, W. M. Brown, P. S. Crozier, P. J. in ‘t Veld, A. Kohlmeyer, S. G. Moore, T. D. Nguyen, R. Shan, M. J. Stevens, J. Tranchida, C. Trott amd S. J. Plimpton, LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm., 271:108171, 2022,

    1. Stillinger, and T. A. Weber, Computer simulation of local order in condensed phases of silicon, Phys. Rev. B, 31(8):5262, 1985,

  1. Scherer, and D. Andrienko, Understanding three-body contributions to coarse-grained force fields, Phys. Chem. Chem. Phys, 20(34):22387–22394, 2018,