Bibliography¶
- Ruehle:2009.a
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:1995
Lyubartsev, Ap And Laaksonen, A, Calculation Of Effective Interaction Potentials From Radial-Distribution Functions - A Reverse Monte-Carlo Approach, Phys. Rev. E
- Tschoep:1998
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:2003
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:2005
Izvekov, S and Voth, GA, Multiscale coarse graining of liquid-state systems, J. Chem. Phys., https://dx.doi.org/10.1063/1.2038787
- Noid:2008.1
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.
- gromacs4
Chem. Theo. Comp., 2008, https://dx.doi.org/10.1021/ct700301q
- Murtola:2007
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:2009
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:2009
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:2012
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
- ruhle2011hybrid
Rühle, Victor and Junghans, Christoph, Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane, Macromolecular Theory and Simulations, 2011
- mashayakrelative
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
- Shell2008
Shell, M Scott, {The relative entropy is fundamental to multiscale and inverse thermodynamic problems.}, The Journal of chemical physics
- Wu2005
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_coarse-graining_2011
Rudzinski, Joseph F. and Noid, W. G., Coarse-graining entropy, forces, and structures, The Journal of Chemical Physics, 2011
- Chaimovich2011
Chaimovich, Aviel and Shell, M. Scott, {Coarse-graining errors and numerical optimization using a relative entropy framework}, The Journal of Chemical Physics
- lyubartsev2010systematic
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_coarse-graining_2014
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
- deOliveira:2016
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:1951
Kirkwood, John G. and Buff, Frank P., The Statistical Mechanical Theory of Solutions. I, The Journal of Chemical Physics, 1951
- Delbary:2020
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:2021
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
- lammps
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