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Molecular Physics
An International Journal at the Interface Between Chemistry and Physics
Volume 111, 2013 - Issue 8
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Research Articles

A simple and effective Verlet-type algorithm for simulating Langevin dynamics

Niels Grønbech-Jensen Department of Mechanical and Aerospace Engineering, University of California, Davis, California, 95616, USA; Department of Chemical Engineering and Materials Science, University of California, Davis, California, 95616, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
&
Oded Farago Department of Mechanical and Aerospace Engineering, University of California, Davis, California, 95616, USA; Department of Biomedical Engineering, Ben Gurion University of the Negev, Be’er Sheva, 84105, Israel; Ilse Katz Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Be’er Sheva, 84105, Israel
Pages 983-991 | Received 17 Nov 2012, Accepted 06 Dec 2012, Published online: 14 Feb 2013

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Crossref
De-zhang Li, Zi-fei Chen, Zhi-jun Zhang & Jian Liu. (2017) Understanding Molecular Dynamics with Stochastic Processes via Real or Virtual Dynamics. Chinese Journal of Chemical Physics 30:6, pages 735-760.
Crossref
Dezhang Li, Xu Han, Yichen Chai, Cong Wang, Zhijun Zhang, Zifei Chen, Jian Liu & Jiushu Shao. (2017) Stationary state distribution and efficiency analysis of the Langevin equation via real or virtual dynamics. The Journal of Chemical Physics 147:18.
Crossref
Jason P. Koski, Robert C. FerrierJr.Jr., Nadia M. Krook, Huikuan Chao, Russell J. Composto, Amalie L. Frischknecht & Robert A. Riggleman. (2017) Comparison of Field-Theoretic Approaches in Predicting Polymer Nanocomposite Phase Behavior. Macromolecules 50:21, pages 8797-8809.
Crossref
Benjamin Beeler, Michael Baskes, David Andersson, Michael W.D. Cooper & Yongfeng Zhang. (2017) A modified Embedded-Atom Method interatomic potential for uranium-silicide. Journal of Nuclear Materials 495, pages 267-276.
Crossref
Chunming Liu, Kaori Kubo, Endian Wang, Kyu-Sung Han, Feng YangGuanqun ChenFernando A. Escobedo, Geoffrey W. Coates & Peng Chen. (2017) Single polymer growth dynamics. Science 358:6361, pages 352-355.
Crossref
Stanard Mebwe Pachong & Kristian K. Müller-Nedebock. (2017) Active force maintains the stability of a contractile ring. The European Physical Journal E 40:10.
Crossref
Oded Farago. (2017) Noise-induced drift in two-dimensional anisotropic systems. Physical Review E 96:4.
Crossref
Francesco Di Maiolo, Matteo Masino & Anna Painelli. (2017) Terahertz-pulse driven modulation of electronic spectra: Modeling electron-phonon coupling in charge-transfer crystals. Physical Review B 96:7.
Crossref
Cameron Sobie, Laurent Capolungo, David L. McDowell & Enrique Martinez. (2017) Scale transition using dislocation dynamics and the nudged elastic band method. Journal of the Mechanics and Physics of Solids 105, pages 161-178.
Crossref
Zhijun Zhang, Xinzijian Liu, Zifei Chen, Haifeng Zheng, Kangyu Yan & Jian Liu. (2017) A unified thermostat scheme for efficient configurational sampling for classical/quantum canonical ensembles via molecular dynamics. The Journal of Chemical Physics 147:3.
Crossref
Henry C. Herbol, James Stevenson & Paulette Clancy. (2017) Computational Implementation of Nudged Elastic Band, Rigid Rotation, and Corresponding Force Optimization. Journal of Chemical Theory and Computation 13:7, pages 3250-3259.
Crossref
Eitam Arnon, Eran Rabani, Daniel Neuhauser & Roi Baer. (2017) Equilibrium configurations of large nanostructures using the embedded saturated-fragments stochastic density functional theory. The Journal of Chemical Physics 146:22.
Crossref
Gerhard Jung, Martin Hanke & Friederike Schmid. (2017) Iterative Reconstruction of Memory Kernels. Journal of Chemical Theory and Computation 13:6, pages 2481-2488.
Crossref
Félix Mouhat, Sandro Sorella, Rodolphe Vuilleumier, Antonino Marco Saitta & Michele Casula. (2017) Fully Quantum Description of the Zundel Ion: Combining Variational Quantum Monte Carlo with Path Integral Langevin Dynamics. Journal of Chemical Theory and Computation 13:6, pages 2400-2417.
Crossref
Andrea Fortini & Richard P. Sear. (2017) Stratification and Size Segregation of Ternary and Polydisperse Colloidal Suspensions during Drying. Langmuir 33:19, pages 4796-4805.
Crossref
Ovidio Peña-Rodríguez, Alejandro Prada, José Olivares, Alicia Oliver, Luis Rodríguez-Fernández, Héctor G. Silva-Pereyra, Eduardo Bringa, José Manuel Perlado & Antonio Rivera. (2017) Understanding the ion-induced elongation of silver nanoparticles embedded in silica. Scientific Reports 7:1.
Crossref
Andrés Córdoba, Daniel M. Hinckley, Joshua Lequieu & Juan J. de Pablo. (2017) A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions. Biophysical Journal 112:7, pages 1302-1315.
Crossref
Andrey A. Kuznetsov & Alexander F. Pshenichnikov. (2017) Sedimentation equilibrium of magnetic nanoparticles with strong dipole-dipole interactions. Physical Review E 95:3.
Crossref
Mihaela Osaci & Matteo Cacciola. (2017) Study about the nanoparticle agglomeration in a magnetic nanofluid by the Langevin dynamics simulation model using an effective Verlet-type algorithm. Microfluidics and Nanofluidics 21:2.
Crossref
Thomas Eisenstecken, Ali Ghavami, Alexander Mair, Gerhard Gompper & Roland G. Winkler. Conformational and dynamical properties of semiflexible polymers in the presence of active noise. Conformational and dynamical properties of semiflexible polymers in the presence of active noise.
Huikuan Chao, Jason Koski & Robert A. Riggleman. (2017) Solvent vapor annealing in block copolymer nanocomposite films: a dynamic mean field approach. Soft Matter 13:1, pages 239-249.
Crossref
Jeff P. Thompson & Isaac C. Sanchez. (2016) System-size effects in ionic fluids under periodic boundary conditions. The Journal of Chemical Physics 145:21.
Crossref
Masahide Sato. (2016) Effect of direction of an external force on crystallization of colloidal particles in a V-shaped groove by sedimentation. Japanese Journal of Applied Physics 55:9, pages 095601.
Crossref
Carsten Svaneborg, Hossein Ali Karimi-Varzaneh, Nils Hojdis, Frank Fleck & Ralf Everaers. (2016) Multiscale approach to equilibrating model polymer melts. Physical Review E 94:3.
Crossref
Tomohiro Tajiri, Ryosuke Matsuzaki & Yoshinobu Shimamura. (2016) Simulation of water impregnation through vertically aligned CNT forests using a molecular dynamics method. Scientific Reports 6:1.
Crossref
Lane W. Votapka, Christopher T. Lee & Rommie E. Amaro. (2016) Two Relations to Estimate Membrane Permeability Using Milestoning. The Journal of Physical Chemistry B 120:33, pages 8606-8616.
Crossref
Eiji Tsuchida. (2016) An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations. Journal of the Physical Society of Japan 85:8, pages 084801.
Crossref
Evyatar Arad, Oded Farago & Niels Grønbech‐Jensen. (2016) The G‐JF Thermostat for Accurate Configurational Sampling in Soft‐Matter Simulations. Israel Journal of Chemistry 56:8, pages 629-635.
Crossref
Shaked Regev, Niels Grønbech-Jensen & Oded Farago. (2016) Isothermal Langevin dynamics in systems with power-law spatially dependent friction. Physical Review E 94:1.
Crossref
Benjamin Beeler, Mark Asta, Peter Hosemann & Niels Grønbech-Jensen. (2016) Effect of strain and temperature on the threshold displacement energy in body-centered cubic iron. Journal of Nuclear Materials 474, pages 113-119.
Crossref
X. W. Zhou, F. El Gabaly, V. Stavila & M. D. Allendorf. (2016) Molecular Dynamics Simulations of Hydrogen Diffusion in Aluminum. The Journal of Physical Chemistry C 120:14, pages 7500-7509.
Crossref
Xingyu Gao, Jun Fang & Han Wang. (2016) Sampling the isothermal-isobaric ensemble by Langevin dynamics. The Journal of Chemical Physics 144:12.
Crossref
Stefan Paquay & Remy Kusters. (2016) A Method for Molecular Dynamics on Curved Surfaces. Biophysical Journal 110:6, pages 1226-1233.
Crossref
Oded Farago & Niels Grønbech-Jensen. (2016) On the connection between dissipative particle dynamics and the Itô-Stratonovich dilemma. The Journal of Chemical Physics 144:8.
Crossref
C.?L.?N. Oliveira, A.?P. Vieira, D. Helbing, J.?S. Andrade & H.?J. Herrmann. (2016) Keep-Left Behavior Induced by Asymmetrically Profiled Walls. Physical Review X 6:1.
Crossref
Salvador Herrera-Velarde, Gabriel Pérez-Angel & Ramón Castañeda-Priego. (2016) One-dimensional Gaussian-core fluid: ordering and crossover from normal diffusion to single-file dynamics. Soft Matter 12:44, pages 9047-9057.
Crossref
Nadiv Dharan & Oded Farago. (2016) Formation of semi-dilute adhesion domains driven by weak elasticity-mediated interactions. Soft Matter 12:31, pages 6649-6655.
Crossref
Stefan Paquay, Halim Kusumaatmaja, David J. Wales, Roya Zandi & Paul van der Schoot. (2016) Energetically favoured defects in dense packings of particles on spherical surfaces. Soft Matter 12:26, pages 5708-5717.
Crossref
Pedro H. Guimar?es, Gabriel T. Landi & M?rio J. de Oliveira. (2015) Thermal rectification in anharmonic chains under an energy-conserving noise. Physical Review E 92:6.
Crossref
Daniel M. Hinckley & Juan J. de Pablo. (2015) Coarse-Grained Ions for Nucleic Acid Modeling. Journal of Chemical Theory and Computation 11:11, pages 5436-5446.
Crossref
Alexander F. Pshenichnikov & Andrey A. Kuznetsov. (2015) Self-organization of magnetic moments in dipolar chains with restricted degrees of freedom. Physical Review E 92:4.
Crossref
G. Linga, P. Ballone & Alex Hansen. (2015) Creep rupture of fiber bundles: A molecular dynamics investigation. Physical Review E 92:2.
Crossref
Ajay P. ManuelJohn LambertMichael T. Woodside. (2015) Reconstructing folding energy landscapes from splitting probability analysis of single-molecule trajectories. Proceedings of the National Academy of Sciences 112:23, pages 7183-7188.
Crossref
Enrique Martínez, Marc J. Cawkwell, Arthur F. Voter & Anders M. N. Niklasson. (2015) Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics. The Journal of Chemical Physics 142:15.
Crossref
R. L. Davidchack, T. E. Ouldridge & M. V. Tretyakov. (2015) New Langevin and gradient thermostats for rigid body dynamics. The Journal of Chemical Physics 142:14.
Crossref
Benjamin Beeler, Mark Asta, Peter Hosemann & Niels Grønbech-Jensen. (2015) Effects of applied strain on radiation damage generation in body-centered cubic iron. Journal of Nuclear Materials 459, pages 159-165.
Crossref
Bradley C. Hubartt & Jacques G. Amar. (2015) Critical island-size, stability, and morphology of 2D colloidal Au nanoparticle islands. The Journal of Chemical Physics 142:2.
Crossref
Vasileios Prymidis, Harmen Sielcken & Laura Filion. (2015) Self-assembly of active attractive spheres. Soft Matter 11:21, pages 4158-4166.
Crossref
Nandu Gopan & Sarith P. Sathian. (2014) A Langevin dynamics study of nanojets. Journal of Molecular Liquids 200, pages 246-258.
Crossref
Niels Grønbech-Jensen & Oded Farago. (2014) Constant pressure and temperature discrete-time Langevin molecular dynamics. The Journal of Chemical Physics 141:19.
Crossref
Michael?T. Woodside, John Lambert & Kevin?S.D. Beach. (2014) Determining Intrachain Diffusion Coefficients for Biopolymer Dynamics from Single-Molecule Force Spectroscopy Measurements. Biophysical Journal 107:7, pages 1647-1653.
Crossref
Oded Farago & Niels Grønbech-Jensen. (2014) Fluctuation–Dissipation Relation for Systems with Spatially Varying Friction. Journal of Statistical Physics 156:6, pages 1093-1110.
Crossref
Niels Grønbech-Jensen, Natha Robert Hayre & Oded Farago. (2014) Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations. Computer Physics Communications 185:2, pages 524-527.
Crossref
Oded Farago & Niels Grønbech-Jensen. (2014) Langevin dynamics in inhomogeneous media: Re-examining the Itô-Stratonovich dilemma. Physical Review E 89:1.
Crossref

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