Bibliography¶
Rühle and C. Junghans and A. Lukyanov and K. Kremer and D. Andrienko, Versatile Object-oriented Toolkit for Coarse-graining Applications, J. Chem. Theor. Comp., 2009, https://dx.doi.org/10.1021/ct900369w
Lyubartsev, Ap And Laaksonen, A, Calculation Of Effective Interaction Potentials From Radial-Distribution Functions - A Reverse Monte-Carlo Approach, Phys. Rev. E
Tschöp, W and Kremer, K and Batoulis, J and Burger, T and Hahn, O, Simulation of polymer melts. I. Coarse-graining procedure for polycarbonates, Acta Polymerica
Reith, D and Pütz, M and Müller-Plathe, F, Deriving effective mesoscale potentials from atomistic simulations, J. Comp. Chem., https://dx.doi.org/10.1002/jcc.10307
Izvekov, S and Voth, GA, Multiscale coarse graining of liquid-state systems, J. Chem. Phys., https://dx.doi.org/10.1063/1.2038787
Noid, W G and Chu, J and Ayton, G S and Krishna, V and Izvekov, S and Voth, G and Das, A and Andersen, H C, The multiscale coarse graining method. 1. A rigorous bridge between atomistic and coarse-grained models, J. Chem. Phys.
Chem. Theo. Comp., 2008, https://dx.doi.org/10.1021/ct700301q
Murtola, T and Falck, E and Karttunen, M and Vattulainen, I, Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints, J. Chem. Phys., https://dx.doi.org/10.1063/1.2646614
Wang, H and Junghans, C and Kremer, K, Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?, Eur. Phys. J. E, https://dx.doi.org/10.1140/epje/i2008-10413-5
Fritz, Dominik and Harmandaris, Vagelis A. and Kremer, Kurt and van der Vegt, Nico F. A., Coarse-Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities, Macromolecules, 2009
Ganguly, P. and Mukherji, D. and Junghans, C. and van der Vegt, Nico F. A., Kirkwood-Buff coarse-grained force fields for aqueous solutions, J. Chem. Theor. Comp., 2012, https://dx.doi.org/10.1021/ct3000958
Rühle, Victor and Junghans, Christoph, Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane, Macromolecular Theory and Simulations, 2011
Mashayak, SY and Jochum, Mara N and Koschke, Konstantin and Aluru, NR and Rühle, Victor and Junghans, Christoph, Relative entropy and optimization-driven coarse-graining methods in VOTCA, Plos One, 2015, https://dx.doi.org/10.1371/journal.pone.0131754
Shell, M Scott, {The relative entropy is fundamental to multiscale and inverse thermodynamic problems.}, The Journal of chemical physics
Wu, Di and Kofke, David A., {Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation.}, The Journal of chemical physics
Rudzinski, Joseph F. and Noid, W. G., Coarse-graining entropy, forces, and structures, The Journal of Chemical Physics, 2011
Chaimovich, Aviel and Shell, M. Scott, {Coarse-graining errors and numerical optimization using a relative entropy framework}, The Journal of Chemical Physics
Lyubartsev, Alexander and Mirzoev, Alexander and Chen, LiJun and Laaksonen, Aatto, Systematic coarse-graining of molecular models by the Newton inversion method, Faraday discussions, 2010
Lu, Jibao and Qiu, Yuqing and Baron, Riccardo and Molinero, Valeria, Coarse-Graining of {TIP}4P/2005, {TIP}4P-Ew, {SPC}/E, and {TIP}3P to Monatomic Anisotropic Water Models Using Relative Entropy Minimization, Journal of Chemical Theory and Computation, 2014
de Oliveira, Tiago E. and Netz, Paulo A. and Kremer, Kurt and Junghans, Christoph and Mukherji, Debashish, C–IBI: Targeting cumulative coordination within an iterative protocol to derive coarse-grained models of (multi-component) complex fluids, The Journal of Chemical Physics, 2016
Kirkwood, John G. and Buff, Frank P., The Statistical Mechanical Theory of Solutions. I, The Journal of Chemical Physics, 1951
Delbary, M. Hanke and D. Ivanizki, A generalized Newton iteration for computing the solution of the inverse Henderson problem, Inverse Probl. Sci. Eng., 2020, https://dx.doi.org/10.1080/17415977.2019.1710504
Bernhardt, M. Hanke and N. F. A. van der Vegt, Iterative integral equation methods for structural coarse-graining, J. Chem. Phys., 2021, https://dx.doi.org/10.1063/5.0038633
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 (2022) 10817, https://doi.org/10.1016/j.cpc.2021.108171