Advanced search
Publication Cover
Soft Materials Volume 1, 2002 - Issue 1
Submit an article Journal homepage
382
Views
74
CrossRef citations to date
0
Altmetric
Original Articles

On Coarse-Graining by the Inverse Monte Carlo Method: Dissipative Particle Dynamics Simulations Made to a Precise Tool in Soft Matter Modeling

Alexander P. Lyubartsev Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, S-106 91, SwedenCorrespondence[email protected]
,
Mikko Karttunen Biophysics and Statistical Mechanics Group, Laboratory of Computational Engineering, Helsinki University of Technology, P. O. Box 9400, Helsinki, FIN-02015 HUT, Finland
,
Ilpo Vattulainen Laboratory of Physics and Helsinki Institute of Physics, Helsinki University of Technology, P. O. Box 1100, Helsinki, FIN-02015 HUT, Finland
&
Aatto Laaksonen Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, S-106 91, Sweden
Pages 121-137 | Received 17 May 2002, Accepted 17 Jun 2002, Published online: 15 Feb 2007

Citations (74)

Keep up to date with the latest research on this topic with citation updates for this article.

Subscribe to citation updates

Read on this site (3)

Vasilios Raptis, Christos Dimitroulis & Theophanes Raptis. (2021) Just type polyana and press Enter: a post-processing application designed with simplicity of use in mind. Molecular Simulation 47:2-3, pages 284-291.
Read now
Takayuki Kobayashi, Hedong Zhang, Kenji Fukuzawa & Shintaro Itoh. (2020) Effect of transverse dissipative particle dynamics on dynamic properties of nanometer-thick liquid films on solid surfaces. Molecular Simulation 46:16, pages 1281-1290.
Read now
Sabine H. L. Klapp, Jörg R. Silbermann & Martin Schoen. (2007) Dynamics of coarse-grained fluid mixtures: how important is the static structure?. Molecular Physics 105:8, pages 1039-1052.
Read now

Articles from other publishers (71)

Rosa Suárez-López, Víctor F. Puntes, Neus G. Bastús, Carmen Hervés & Carlos Jaime. (2022) Nucleation and growth of gold nanoparticles in the presence of different surfactants. A dissipative particle dynamics study. Scientific Reports 12:1.
Crossref
Maryam Reisjalali, Rex Manurung, Paola Carbone & Alessandro Troisi. (2022) Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors. Molecular Systems Design & Engineering 7:3, pages 294-305.
Crossref
Jiuling Wang, Pieter J. in ’t Veld, Mark O. Robbins & Ting Ge. (2022) Effects of Coarse-Graining on Molecular Simulation of Craze Formation in Polymer Glass. Macromolecules 55:4, pages 1267-1278.
Crossref
Rafael Maglia de Souza, Tuanan C. Lourenço, Leonardo José Amaral de Siqueira, Mikko Karttunen, Juarez L.F. Da Silva & Luis Gustavo Dias. (2021) Development of coarse-grained force field to investigate sodium-ion transport mechanisms in cyanoborate-based ionic liquid. Journal of Molecular Liquids 338, pages 116648.
Crossref
Ting Ge, Jiuling Wang & Mark O. Robbins. (2021) Effects of Coarse-Graining on Molecular Simulations of Mechanical Properties of Glassy Polymers. Macromolecules 54:5, pages 2277-2287.
Crossref
Richard J. Gowers, Paola Carbone & Nicodemo Di Pasquale. (2020) A different approach to dual-scale models. Journal of Computational Physics 413, pages 109465.
Crossref
Kiran Kumari, Burkhard Duenweg, Ranjith Padinhateeri & J. Ravi Prakash. (2020) Computing 3D Chromatin Configurations from Contact Probability Maps by Inverse Brownian Dynamics. Biophysical Journal 118:9, pages 2193-2208.
Crossref
R. M. de Souza, R. H. Ratochinski, Mikko Karttunen & L. G. Dias. (2019) Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles. Journal of Chemical Information and Modeling 60:2, pages 522-536.
Crossref
Marcel Langenberg, Nicholas E. Jackson, Juan J. de Pablo & Marcus Müller. (2018) Role of translational entropy in spatially inhomogeneous, coarse-grained models. The Journal of Chemical Physics 148:9.
Crossref
S. T. John & Gábor Csányi. (2017) Many-Body Coarse-Grained Interactions Using Gaussian Approximation Potentials. The Journal of Physical Chemistry B 121:48, pages 10934-10949.
Crossref
Tonalli Rodríguez-López, Yuriy Khalak & Mikko Karttunen. (2017) Non-conformal coarse-grained potentials for water. The Journal of Chemical Physics 147:13.
Crossref
Berend Christopher Rinderspacher, Jaydeep P. Bardhan & Ahmed E. Ismail. (2017) Theory of wavelet-based coarse-graining hierarchies for molecular dynamics. Physical Review E 96:1.
Crossref
Pep Español & Patrick B. Warren. (2017) Perspective: Dissipative particle dynamics. The Journal of Chemical Physics 146:15.
Crossref
Paolo Mereghetti, Giuseppe Maccari, Giulia Lia Beatrice Spampinato & Valentina Tozzini. (2016) Optimization of Analytical Potentials for Coarse-Grained Biopolymer Models. The Journal of Physical Chemistry B 120:33, pages 8571-8579.
Crossref
Marco Molinari, Andrey V. Brukhno, Stephen C. Parker & Dino Spagnoli. 2016. Molecular Modeling of Geochemical Reactions. Molecular Modeling of Geochemical Reactions 33 75 .
Vagelis Harmandaris, Evangelia Kalligiannaki, Markos Katsoulakis & Petr Plecháč. (2016) Path-space variational inference for non-equilibrium coarse-grained systems. Journal of Computational Physics 314, pages 355-383.
Crossref
Nikolai D. Petsev, L. Gary Leal & M. Scott Shell. (2016) Multiscale simulation of ideal mixtures using smoothed dissipative particle dynamics. The Journal of Chemical Physics 144:8.
Crossref
Behnaz Bagheri, Björn Baumeier & Mikko Karttunen. (2016) Getting excited: challenges in quantum-classical studies of excitons in polymeric systems. Physical Chemistry Chemical Physics 18:44, pages 30297-30304.
Crossref
Stephen Pankavich & Peter Ortoleva. (2015) A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization. Computation 3:1, pages 29-57.
Crossref
Matúš Rebič, Francesca Mocci, Aatto Laaksonen & Jozef Uličný. (2014) Multiscale Simulations of Human Telomeric G-Quadruplex DNA. The Journal of Physical Chemistry B 119:1, pages 105-113.
Crossref
Emanuel K. Peter & Igor V. Pivkin. (2014) A polarizable coarse-grained water model for dissipative particle dynamics. The Journal of Chemical Physics 141:16.
Crossref
Aymeric Naômé, Aatto Laaksonen & Daniel P. Vercauteren. (2014) A Solvent-Mediated Coarse-Grained Model of DNA Derived with the Systematic Newton Inversion Method. Journal of Chemical Theory and Computation 10:8, pages 3541-3549.
Crossref
Markos Katsoulakis, Petr Plecháč, Luc Rey-Bellet & Dimitrios Tsagkarogiannis. (2014) Coarse-graining schemes for stochastic lattice systems with short and long-range interactions. Mathematics of Computation 83:288, pages 1757-1793.
Crossref
Kathryn Farrell & J. Tinsley Oden. (2014) Calibration and validation of coarse-grained models of atomic systems: application to semiconductor manufacturing. Computational Mechanics 54:1, pages 3-19.
Crossref
Anupriya Agrawal, Dipak Aryal, Dvora Perahia, Ting Ge & Gary S. Grest. (2014) Coarse-Graining Atactic Polystyrene and Its Analogues. Macromolecules 47:9, pages 3210-3218.
Crossref
Davit Hakobyan & Andreas Heuer. (2014) Key Molecular Requirements for Raft Formation in Lipid/Cholesterol Membranes. PLoS ONE 9:2, pages e87369.
Crossref
Matthew C. Hagy & Rigoberto Hernandez. (2014) Dynamical simulation of electrostatic striped colloidal particles. The Journal of Chemical Physics 140:3.
Crossref
G. Andrés Cisneros, Mikko Karttunen, Pengyu Ren & Celeste Sagui. (2013) Classical Electrostatics for Biomolecular Simulations. Chemical Reviews 114:1, pages 779-814.
Crossref
Ming-Tsung Lee, Aleksey Vishnyakov & Alexander V. Neimark. (2013) Calculations of Critical Micelle Concentration by Dissipative Particle Dynamics Simulations: The Role of Chain Rigidity. The Journal of Physical Chemistry B 117:35, pages 10304-10310.
Crossref
Markos A. Katsoulakis & Petr Plecháč. (2013) Information-theoretic tools for parametrized coarse-graining of non-equilibrium extended systems. The Journal of Chemical Physics 139:7.
Crossref
Matthew C. Hagy & Rigoberto Hernandez. (2013) Dynamical simulation of dipolar Janus colloids: Dynamical properties. The Journal of Chemical Physics 138:18.
Crossref
Aleksey Vishnyakov, Ming-Tsung Lee & Alexander V. Neimark. (2013) Prediction of the Critical Micelle Concentration of Nonionic Surfactants by Dissipative Particle Dynamics Simulations. The Journal of Physical Chemistry Letters 4:5, pages 797-802.
Crossref
P. Ortoleva, A. Singharoy & S. Pankavich. (2013) Hierarchical multiscale modeling of macromolecules and their assemblies. Soft Matter 9:16, pages 4319.
Crossref
Yong-Lei Wang, Alexander Lyubartsev, Zhong-Yuan Lu & Aatto Laaksonen. (2013) Multiscale coarse-grained simulations of ionic liquids: comparison of three approaches to derive effective potentials. Physical Chemistry Chemical Physics 15:20, pages 7701.
Crossref
Zhong-Yuan Lu & Yong-Lei Wang. 2013. Biomolecular Simulations. Biomolecular Simulations 617 633 .
W. G. Noid. 2013. Biomolecular Simulations. Biomolecular Simulations 487 531 .
T. Hynninen, C.L. Dias, A. Mkrtchyan, V. Heinonen, M. Karttunen, A.S. Foster & T. Ala-Nissila. (2012) A molecular dynamics implementation of the 3D Mercedes-Benz water model. Computer Physics Communications 183:2, pages 363-369.
Crossref
Evangelia Kalligiannaki, Markos A. Katsoulakis & Petr Plecháč. 2012. Numerical Analysis of Multiscale Computations. Numerical Analysis of Multiscale Computations 235 257 .
Victor Rühle & Christoph Junghans. (2011) Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane. Macromolecular Theory and Simulations 20:7, pages 472-477.
Crossref
Piotr Kowalczyk, Piotr A. Gauden & Alina Ciach. (2011) Optimization of Coarse-Grained Interaction Potential: Inside Inherent Limitations of Coarse-Graining Methods. The Journal of Physical Chemistry B 115:21, pages 6985-6994.
Crossref
J. W. Mullinax & W. G. Noid. (2009) A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials. The Journal of Physical Chemistry C 114:12, pages 5661-5674.
Crossref
P. Español. (2009) Hybrid description of complex molecules. EPL (Europhysics Letters) 88:4, pages 40008.
Crossref
Piotr Kowalczyk, Piotr A. Gauden & Alina Ciach. (2009) Role of Short-Range Directional Interactions in Coarse-Graining of Protic/Aprotic Liquids. The Journal of Physical Chemistry B 113:39, pages 12988-12998.
Crossref
Cristiano L. Dias, Tapio Ala-Nissila, Martin Grant & Mikko Karttunen. (2009) Three-dimensional “Mercedes-Benz” model for water. The Journal of Chemical Physics 131:5.
Crossref
A. Eriksson, M. Nilsson Jacobi, J. Nyström & K. Tunstrøm. (2009) On the microscopic foundation of dissipative particle dynamics. EPL (Europhysics Letters) 86:4, pages 44001.
Crossref
Anders Eriksson, Martin Nilsson Jacobi, Johan Nyström & Kolbjørn Tunstrøm. (2009) Bottom-up derivation of an effective thermostat for united atoms simulations of water. The Journal of Chemical Physics 130:16.
Crossref
Anders Eriksson, Martin Nilsson Jacobi, Johan Nyström & Kolbjørn Tunstrøm. (2009) A method for estimating the interactions in dissipative particle dynamics from particle trajectories. Journal of Physics: Condensed Matter 21:9, pages 095401.
Crossref
Han Wang, Christoph Junghans & Kurt Kremer. (2009) Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining?. The European Physical Journal E 28:2, pages 221-229.
Crossref
Yanting Wang, W. G. Noid, Pu Liu & Gregory A. Voth. (2009) Effective force coarse-graining. Physical Chemistry Chemical Physics 11:12, pages 2002.
Crossref
Mikko Karttunen, Teemu Murtola & Ilpo Vattulainen. 2008. Coarse-Graining of Condensed Phase and Biomolecular Systems. Coarse-Graining of Condensed Phase and Biomolecular Systems 83 106 .
Elaine Chan, Sharon Glotzer, Peter Cummings, Clare McCabe & Alberto Striolo. 2008. Coarse-Graining of Condensed Phase and Biomolecular Systems. Coarse-Graining of Condensed Phase and Biomolecular Systems 415 431 .
Anders Eriksson, Martin Nilsson Jacobi, Johan Nyström & Kolbjørn Tunstrøm. (2008) Effective thermostat induced by coarse graining of simple point charge water. The Journal of Chemical Physics 129:2.
Crossref
Reinier L. C. Akkermans. (2008) Mesoscale model parameters from molecular cluster calculations. The Journal of Chemical Physics 128:24.
Crossref
Anders Eriksson, Martin Nilsson Jacobi, Johan Nyström & Kolbjørn Tunstrøm. (2008) Using force covariance to derive effective stochastic interactions in dissipative particle dynamics. Physical Review E 77:1.
Crossref
Maria Sammalkorpi, Mikko Karttunen & Mikko Haataja. (2007) Structural Properties of Ionic Detergent Aggregates:  A Large-Scale Molecular Dynamics Study of Sodium Dodecyl Sulfate. The Journal of Physical Chemistry B 111:40, pages 11722-11733.
Crossref
Elaine R. Chan, Alberto Striolo, Clare McCabe, Peter T. Cummings & Sharon C. Glotzer. (2007) Coarse-grained force field for simulating polymer-tethered silsesquioxane self-assembly in solution. The Journal of Chemical Physics 127:11.
Crossref
Gergely Tóth. (2007) Interactions from diffraction data: historical and comprehensive overview of simulation assisted methods. Journal of Physics: Condensed Matter 19:33, pages 335220.
Crossref
P.G. Kusalik, K. Gillis & J. Vatamanu. (2007) Utilizing Averaged Configuations from Molecular Dynamics Simulation Trajectories. Utilizing Averaged Configuations from Molecular Dynamics Simulation Trajectories.
Petri Nikunen, Ilpo Vattulainen & Mikko Karttunen. (2007) Reptational dynamics in dissipative particle dynamics simulations of polymer melts. Physical Review E 75:3.
Crossref
Teemu Murtola, Emma Falck, Mikko Karttunen & Ilpo Vattulainen. (2007) Coarse-grained model for phospholipid/cholesterol bilayer employing inverse Monte Carlo with thermodynamic constraints. The Journal of Chemical Physics 126:7.
Crossref
Teemu Murtola, Mikko Kupiainen, Emma Falck & Ilpo Vattulainen. (2007) Conformational analysis of lipid molecules by self-organizing maps. The Journal of Chemical Physics 126:5.
Crossref
K. Gillis, J. Vatamanu, M. S. Gulam Razul & Peter G. Kusalik. 2007. Applied Parallel Computing. State of the Art in Scientific Computing. Applied Parallel Computing. State of the Art in Scientific Computing 51 58 .
Li-Jun Chen, Hu-Jun Qian, Zhong-Yuan Lu, Ze-Sheng Li & Chia-Chung Sun. (2006) An Automatic Coarse-Graining and Fine-Graining Simulation Method:  Application on Polyethylene. The Journal of Physical Chemistry B 110:47, pages 24093-24100.
Crossref
Jörg R. Silbermann, Sabine H. L. Klapp, Martin Schoen, Naresh Chennamsetty, Henry Bock & Keith E. Gubbins. (2006) Mesoscale modeling of complex binary fluid mixtures: Towards an atomistic foundation of effective potentials. The Journal of Chemical Physics 124:7.
Crossref
René Pool & Peter G. Bolhuis. (2006) Can purely repulsive soft potentials predict micelle formation correctly?. Phys. Chem. Chem. Phys. 8:8, pages 941-948.
Crossref
Stefan M. Kast, Wulf Hauptmann & Bernd Schilling. (2006) Design of reduced molecular models by integral equation theory. Chemical Physics Letters 418:1-3, pages 202-207.
Crossref
E. Salonen, E. Terama, I. Vattulainen & M. Karttunen. (2005) Dielectrophoresis of nanocolloids: A molecular dynamics study. The European Physical Journal E 18:2, pages 133-142.
Crossref
George A. Khelashvili, Sagar A. Pandit & H. L. Scott. (2005) Self-consistent mean-field model based on molecular dynamics: Application to lipid-cholesterol bilayers. The Journal of Chemical Physics 123:3.
Crossref
Teemu Murtola, Emma Falck, Michael Patra, Mikko Karttunen & Ilpo Vattulainen. (2004) Coarse-grained model for phospholipid/cholesterol bilayer. The Journal of Chemical Physics 121:18, pages 9156-9165.
Crossref
Michael Patra & Mikko Karttunen. (2004) Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: Diffusion, free energy of hydration, and structural properties. Journal of Computational Chemistry 25:5, pages 678-689.
Crossref
P Nikunen, M Karttunen & I Vattulainen. (2003) How would you integrate the equations of motion in dissipative particle dynamics simulations?. Computer Physics Communications 153:3, pages 407-423.
Crossref

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.