Langevin Dynamics in Constant Pressure Extended Systems
|
|
- Mercy Kennedy
- 5 years ago
- Views:
Transcription
1 Langevin Dynamics in Constant Pressure Extended Systems D. Quigley and M.I.J. Probert CMMP
2 Talk Outline Molecular dynamics and ensembles. Existing methods for sampling at NPT. Langevin dynamics in constant pressure systems. Results classical and ab-initio. Conclusions. 2
3 MD and Ensembles MD models dynamical properties of a system using numerical integration of classical equations of motion. Computationally limited to simulating a small number of particles to represent a sample of the larger system. Should be subject to both temperature and density fluctuations due to exchange of energy and particles with the rest of the system. EOMs must sample phase space with correct probability requires ergodicity. Therm al Fluctuations - NVT + density (volum e) fluctuations NPT Ensem ble 3
4 Solutions Equilibrium density fluctuations (barostat) Extended system with volume/cell vectors as dynamical variable. Either Hoover (isotropic) or Parrinello-Rahman (anisotropic). Number of atoms remains constant density fluctuates Equilibrium temperature fluctuations (thermostat) Ergodicity requires chaotic behaviour. Standard method is Nosé-Hoover chains. Deterministic and simple requires chaotic behaviour to be provided by the atomic system I.e. need large N! Large N not feasible for ab-initio MD. Is there an alternative? 4
5 Langevin Dynamics (LD) Convert Hamilton s EOM for p into Langevin equation. Dam ping + stochastic buffeting Balancing the two new terms generates thermal equilibrium. Langevin thermostat correct temperature fluctuations with no ergodicity problems. BUT no equivalent method of producing density fluctuations. What would happen if we could perform LD in a pressure regulating extended system? 1. Would it give the correct E & fluctuations (NPT ensemble?) 2. What would be the advantages of doing this? 5
6 Hoover system Expansion and contraction of system shape of simulation cell constant. Have two extra phase space co-ordinates volume V and a momentum p (strain rate x fictitious volume mass W). Particle motions are coupled to the box momentum. X is the deterministic part of the internal pressure 6
7 Yes it does sample the NPT ensemble! Construct Fokker-Planck equations for the EOMs continuity equation for probability density in the extended phase space. This has the desired probability density as a solution. Equations correctly sample the NPT ensemble. Complications The Hoover equations conserve the quantity BUT, this is not a Hamiltonian. No Hamiltonian can be written down for the Hoover system. Probability of equal energy configurations may not be equal. See Tuckerman et al Europhys Lett 45 p149 (1999). Implies probability gradients imbalances Langevin dynamics. Analysis shows not a problem for Hoover system. 7
8 Parrinello-Rahman System Allows size and shape to change anisotopic fluctuations. Dynamical co-ordinate + momentum for each component of 3 cell vectors. X is deterministic part of pressure tensor. Again non-hamiltonian. In this case probability gradients prohibit Langevin dynamics of the cell variable not crucial to correct sampling. 8
9 Parameters Langevin damping co-efficient or thermostat relaxation time 1/. Fictitious mass W of the cell variable(s), corresponds to cell relaxation time. MD regime LD regime 0 identified from bulk memory function. See Kneller and Hinsen J.Chem.Phys 115(24) p11097 (2001) Choose cell paramter W based on e.g. velocity spectrum. Integration Algorithm Developed from Louiville operators for the extended system. Leads to Verlet-like algorithm reversible in zero friction limit. For details see Quigley & Probert J.Chem.Phys 2004 (In Press) matter/
10 Classical Core Softened Potentials Mapping of the Stell-Hemm er phase diagram (pair potential) Both runs seeking 600 K, 5 MPa with equal relaxation times No prior knowledge of dynamics. Langevin dynamics in the Hoover Ensem ble. Conventional Nosé-Hoover chain based constant pressure schem e. 10
11 CASTEP - Silicon (isotropic) Simulated using the optimal damping coefficient identified from a bulk sim ulation using the Tersoff potential. 8,400 time-steps ( t = 8 fs) at 293 K 1 atm. Using E xc = E LDA E cut-off = 160 ev (ultrasofts) 8 atom cell 2x2x2 MP k-point grid Volume fluctuations yield K T =103.5 ± 5.2 GPa c.f. experiment 102 GPa and equivalent Nosé-Hoover run (not converged at this run length) K T =58.7 GPa! 11
12 CASTEP - P 2 I 4 (Fully Flexible) Triclinic cell, a b c. No prior knowledge of dynamics use conservative and W from earlier work on elemental P and I (running in LD regime). Good results without prior knowledge of memory function or ideal W - 20,000 timesteps ( t = 8fs) at 250 K, 50 MPa. 12
13 Conclusions Langevin dynamics in the Hoover or Parrinello-Rahman system is a valid method for sampling the NPT ensemble. This method has been tested in a classical MD code and implemented in the plane wave DFT code CASTEP. Langevin NPT has statistical efficiency advantages over Nosé- Hoover based schemes. reduced correlation times guaranteed ergodicity on shorter timescales Further details see D. Quigley and M.I.J Probert J.Chem.Phys (2004) (in press). matter/
Classical Molecular Dynamics
Classical Molecular Dynamics Matt Probert Condensed Matter Dynamics Group Department of Physics, University of York, U.K. http://www-users.york.ac.uk/~mijp1 Overview of lecture n Motivation n Types of
More informationA Brief Introduction to Ab Initio Molecular Dynamics
A Brief Introduction to Ab Initio Molecular Dynamics Matt Probert Condensed Matter Dynamics Group, University of York, UK http://www.cmt.york.ac.uk/cmd http://www.castep.org Overview of Talk In this talk
More informationAb initio molecular dynamics and nuclear quantum effects
Ab initio molecular dynamics and nuclear quantum effects Luca M. Ghiringhelli Fritz Haber Institute Hands on workshop density functional theory and beyond: First principles simulations of molecules and
More informationTemperature and Pressure Controls
Ensembles Temperature and Pressure Controls 1. (E, V, N) microcanonical (constant energy) 2. (T, V, N) canonical, constant volume 3. (T, P N) constant pressure 4. (T, V, µ) grand canonical #2, 3 or 4 are
More informationJavier Junquera. Statistical mechanics
Javier Junquera Statistical mechanics From the microscopic to the macroscopic level: the realm of statistical mechanics Computer simulations Thermodynamic state Generates information at the microscopic
More informationAb initio molecular dynamics. Simone Piccinin CNR-IOM DEMOCRITOS Trieste, Italy. Bangalore, 04 September 2014
Ab initio molecular dynamics Simone Piccinin CNR-IOM DEMOCRITOS Trieste, Italy Bangalore, 04 September 2014 What is MD? 1) Liquid 4) Dye/TiO2/electrolyte 2) Liquids 3) Solvated protein 5) Solid to liquid
More informationMD Thermodynamics. Lecture 12 3/26/18. Harvard SEAS AP 275 Atomistic Modeling of Materials Boris Kozinsky
MD Thermodynamics Lecture 1 3/6/18 1 Molecular dynamics The force depends on positions only (not velocities) Total energy is conserved (micro canonical evolution) Newton s equations of motion (second order
More informationTemperature and Pressure Controls
Ensembles Temperature and Pressure Controls 1. (E, V, N) microcanonical (constant energy) 2. (T, V, N) canonical, constant volume 3. (T, P N) constant pressure 4. (T, V, µ) grand canonical #2, 3 or 4 are
More informationHigh-throughput Simulations of Shock-waves Using MD. Jacob Wilkins University of York
High-throughput Simulations of Using MD Jacob Wilkins University of York jacob.wilkins@york.ac.uk Mar 2018 Outline 1 2 3 4 5 What are shock-waves? are pressure-waves moving through material faster than
More informationAb initio Molecular Dynamics Born Oppenheimer and beyond
Ab initio Molecular Dynamics Born Oppenheimer and beyond Reminder, reliability of MD MD trajectories are chaotic (exponential divergence with respect to initial conditions), BUT... With a good integrator
More informationWhat is Classical Molecular Dynamics?
What is Classical Molecular Dynamics? Simulation of explicit particles (atoms, ions,... ) Particles interact via relatively simple analytical potential functions Newton s equations of motion are integrated
More informationConstant Pressure Langevin Dynamics: Theory and Application to the Study of Phase Behaviour in Core-Softened Systems.
Constant Pressure Langevin Dynamics: Theory and Application to the Study of Phase Behaviour in Core-Softened Systems. David Quigley A thesis submitted for the degree of Doctor of Philosophy University
More informationIntroduction to Computer Simulations of Soft Matter Methodologies and Applications Boulder July, 19-20, 2012
Introduction to Computer Simulations of Soft Matter Methodologies and Applications Boulder July, 19-20, 2012 K. Kremer Max Planck Institute for Polymer Research, Mainz Overview Simulations, general considerations
More informationIonic Liquids simulations : obtention of structural and transport properties from molecular dynamics. C. J. F. Solano, D. Beljonne, R.
Ionic Liquids simulations : obtention of structural and transport properties from molecular dynamics C. J. F. Solano, D. Beljonne, R. Lazzaroni Ionic Liquids simulations : obtention of structural and transport
More informationQuantum (Path Integral) Molecular Dynamics
Quantum (Path Integral) Molecular Dynamics Matt Probert Condensed Matter Dynamics Group Department of Physics, University of York, U.K. http://www-users.york.ac.uk/~mijp1 Overview of lecture n Background
More informationUniversities of Leeds, Sheffield and York
promoting access to White Rose research papers Universities of Leeds, Sheffield and York http://eprints.whiterose.ac.uk/ Paper published in Zeitschrift für Kristallographie. White Rose Research Online
More informationSupplementary Materials
Supplementary Materials Atomistic Origin of Brittle Failure of Boron Carbide from Large Scale Reactive Dynamics Simulations; Suggestions toward Improved Ductility Qi An and William A. Goddard III * Materials
More informationEnergy and Forces in DFT
Energy and Forces in DFT Total Energy as a function of nuclear positions {R} E tot ({R}) = E DF T ({R}) + E II ({R}) (1) where E DF T ({R}) = DFT energy calculated for the ground-state density charge-density
More informationGeometry Optimisation
Geometry Optimisation Matt Probert Condensed Matter Dynamics Group Department of Physics, University of York, UK http://www.cmt.york.ac.uk/cmd http://www.castep.org Motivation Overview of Talk Background
More informationIntroduction to atomic scale simulations
Powder Technology course Autumn semester 2017 Introduction to atomic scale simulations Peter M Derlet Condensed Matter Theory Paul Scherrer Institut peter.derlet@psi.ch Outline of lecture The big picture
More information4. The Green Kubo Relations
4. The Green Kubo Relations 4.1 The Langevin Equation In 1828 the botanist Robert Brown observed the motion of pollen grains suspended in a fluid. Although the system was allowed to come to equilibrium,
More informationAPMA 2811T. By Zhen Li. Today s topic: Lecture 2: Theoretical foundation and parameterization. Sep. 15, 2016
Today s topic: APMA 2811T Dissipative Particle Dynamics Instructor: Professor George Karniadakis Location: 170 Hope Street, Room 118 Time: Thursday 12:00pm 2:00pm Dissipative Particle Dynamics: Foundation,
More informationMustafa Uludogan 1, Tahir Cagin, William A. Goddard, III Materials and Process Simulation Center, Caltech, Pasadena, CA 91125, U.S.A.
Ab Initio Studies On Phase Behavior of Barium Titanate Mustafa Uludogan 1, Tahir Cagin, William A. Goddard, III Materials and Process Simulation Center, Caltech, Pasadena, CA 91125, U.S.A. 1 Physics Department,
More informationModeling Materials. Continuum, Atomistic and Multiscale Techniques. gg CAMBRIDGE ^0 TADMOR ELLAD B. HHHHM. University of Minnesota, USA
HHHHM Modeling Materials Continuum, Atomistic and Multiscale Techniques ELLAD B. TADMOR University of Minnesota, USA RONALD E. MILLER Carleton University, Canada gg CAMBRIDGE ^0 UNIVERSITY PRESS Preface
More informationComprehensive Nuclear Materials Modelling Section (R. Stoller, Editor) Chapter 128 Molecular Dynamics.
draft 5/10/10 revised SY 12/5/10 Comprehensive Nuclear Materials Modelling Section (R. Stoller, Editor) Chapter 128 Molecular Dynamics Wei Cai 1, Ju Li 2, Sidney Yip 3 1 Department of Mechanical Engineering,
More informationThermal and Mechanical Properties of Pt-Rh Alloys
arxiv:cond-mat/9611241v1 [cond-mat.mtrl-sci] 28 Nov 1996 Thermal and Mechanical Properties of Pt-Rh Alloys G. Dereli, T. Çağın, M. Uludoğan, M. Tomak Department of Physics, Middle East Technical University,
More informationAb Ini'o Molecular Dynamics (MD) Simula?ons
Ab Ini'o Molecular Dynamics (MD) Simula?ons Rick Remsing ICMS, CCDM, Temple University, Philadelphia, PA What are Molecular Dynamics (MD) Simulations? Technique to compute statistical and transport properties
More informationSupporting Information Soft Nanoparticles: Nano Ionic Networks of Associated Ionic Polymers
Electronic Supplementary Material (ESI) for Nanoscale. This journal is The Royal Society of Chemistry 2016 Supporting Information Soft Nanoparticles: Nano Ionic Networks of Associated Ionic Polymers Dipak
More informationAb initio molecular dynamics
Ab initio molecular dynamics Molecular dynamics Why? allows realistic simulation of equilibrium and transport properties in Nature ensemble averages can be used for statistical mechanics time evolution
More informationStatistical methods in atomistic computer simulations
Statistical methods in atomistic computer simulations Prof. Michele Ceriotti, michele.ceriotti@epfl.ch This course gives an overview of simulation techniques that are useful for the computational modeling
More informationarxiv: v1 [cond-mat.stat-mech] 28 Mar 2008
Canonical sampling through velocity-rescaling Giovanni Bussi, Davide Donadio, and Michele Parrinello Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via
More informationarxiv: v1 [physics.chem-ph] 24 Apr 2018
arxiv:1804.08913v1 [physics.chem-ph] 24 Apr 2018 Fast-Forward Langevin Dynamics with Momentum Flips Mahdi Hijazi, 1 David M. Wilkins, 1, a) and Michele Ceriotti 1 Laboratory of Computational Science and
More informationShear Properties and Wrinkling Behaviors of Finite Sized Graphene
Shear Properties and Wrinkling Behaviors of Finite Sized Graphene Kyoungmin Min, Namjung Kim and Ravi Bhadauria May 10, 2010 Abstract In this project, we investigate the shear properties of finite sized
More informationComputer Simulation of Shock Waves in Condensed Matter. Matthew R. Farrow 2 November 2007
Computer Simulation of Shock Waves in Condensed Matter Matthew R. Farrow 2 November 2007 Outline of talk Shock wave theory Results Conclusion Computer simulation of shock waves Shock Wave Theory Shock
More informationDensity Functional Theory: from theory to Applications
Density Functional Theory: from theory to Applications Uni Mainz May 14, 2012 All electrons vs pseudopotentials Classes of Basis-set Condensed phase: Bloch s th and PBC Hamann-Schlüter-Chiang pseudopotentials
More informationThermostatic Controls for Noisy Gradient Systems and Applications to Machine Learning
Thermostatic Controls for Noisy Gradient Systems and Applications to Machine Learning Ben Leimkuhler University of Edinburgh Joint work with C. Matthews (Chicago), G. Stoltz (ENPC-Paris), M. Tretyakov
More informationFrom Physical Modelling to Big Data Analytics: Examples and Challenges
From Physical Modelling to Big Data Analytics: Examples and Challenges Ben Leimkuhler University of Edinburgh EPSRC/NSF ERC ATI Summit on Big Data in the Physical Sciences Outline Part I: Challenges Ideas
More informationOptimization Methods via Simulation
Optimization Methods via Simulation Optimization problems are very important in science, engineering, industry,. Examples: Traveling salesman problem Circuit-board design Car-Parrinello ab initio MD Protein
More informationMolecular Dynamics Simulation of a Nanoconfined Water Film
Molecular Dynamics Simulation of a Nanoconfined Water Film Kyle Lindquist, Shu-Han Chao May 7, 2013 1 Introduction The behavior of water confined in nano-scale environment is of interest in many applications.
More information7 To solve numerically the equation of motion, we use the velocity Verlet or leap frog algorithm. _ V i n = F i n m i (F.5) For time step, we approxim
69 Appendix F Molecular Dynamics F. Introduction In this chapter, we deal with the theories and techniques used in molecular dynamics simulation. The fundamental dynamics equations of any system is the
More informationMechanical Properties of Phagraphene Membranes: A Fully Atomistic Molecular Dynamics Investigation
Mechanical Properties of Phagraphene Membranes: A Fully Atomistic Molecular Dynamics Investigation J. M. de Sousa 1,2, A. L. Aguiar 2, E. C. Girão 2, Alexandre F. Fonseca 1, A. G. Sousa Filho 3, and Douglas
More informationAb initio Molecular Dynamics
Ab initio Molecular Dynamics Jürg Hutter Department of Chemistry, University of Zurich Overview Equations of motion and Integrators General Lagrangian for AIMD Car Parrinello MD and Born Oppenheimer MD
More informationGeneralized valence bond molecular dynamics at constant temperature
M o l e c u l a r Ph y s i c s, 1996, Vo l. 89, No. 5, 1265± 1276 Generalized valence bond molecular dynamics at constant temperature By DOUGLAS A. GIBSON and EM ILY A. CARTER D epartment of Chemistry
More informationElectronic structure simulations of water solid interfaces
Electronic structure simulations of water solid interfaces Angelos Michaelides London Centre for Nanotechnology & Department of Chemistry, University College London www.chem.ucl.ac.uk/ice Main co-workers:
More informationDiffusion of Water and Diatomic Oxygen in Poly(3-hexylthiophene) Melt: A Molecular Dynamics Simulation Study
Diffusion of Water and Diatomic Oxygen in Poly(3-hexylthiophene) Melt: A Molecular Dynamics Simulation Study Julia Deitz, Yeneneh Yimer, and Mesfin Tsige Department of Polymer Science University of Akron
More informationSUPPLEMENTARY MATERIAL. Supplementary material and methods:
Electronic Supplementary Material (ESI) for Catalysis Science & Technology. This journal is The Royal Society of Chemistry 2015 SUPPLEMENTARY MATERIAL Supplementary material and methods: - Computational
More informationSTRONG CONFIGURATIONAL DEPENDENCE OF ELASTIC PROPERTIES OF A CU-ZR BINARY MODEL METALLIC GLASS
Chapter 3 STRONG CONFIGURATIONAL DEPENDENCE OF ELASTIC PROPERTIES OF A CU-ZR BINARY MODEL METALLIC GLASS We report the strong dependence of elastic properties on configurational changes in a Cu-Zr binary
More informationTHERMOSTATS AND THERMAL TRANSPORT IN SOLIDS
Hands-On Tutorial Workshop, July 19 th 2011 THERMOSTATS AND THERMAL TRANSPORT IN SOLIDS Christian Carbogno FRITZ-HABER-INSTITUT DER MAX-PLANCK-GESELLSCHAFT, BERLIN - GERMANY Hands-On Tutorial Workshop,
More informationPractical calculations using first-principles QM Convergence, convergence, convergence
Practical calculations using first-principles QM Convergence, convergence, convergence Keith Refson STFC Rutherford Appleton Laboratory September 18, 2007 Results of First-Principles Simulations..........................................................
More informationDensity Functional Theory
Density Functional Theory Iain Bethune EPCC ibethune@epcc.ed.ac.uk Overview Background Classical Atomistic Simulation Essential Quantum Mechanics DFT: Approximations and Theory DFT: Implementation using
More informationComparison of COMPASS and PCFF in Calculating Mechanical Behaviors of Aramid Fiber by Means of Molecular Dynamics
AMSE JOURNALS-AMSE IIETA publication-2017-series: Modelling B; Vol. 86; N 2; pp 438-446 Submitted Mar. 04; Revised May 12, 2017; Accepted Jun. 12, 2017 Comparison of COMPASS and PCFF in Calculating Mechanical
More informationSet the initial conditions r i. Update neighborlist. r i. Get new forces F i
Set the initial conditions r i t 0, v i t 0 Update neighborlist Get new forces F i r i Solve the equations of motion numerically over time step t : r i t n r i t n + v i t n v i t n + Perform T, P scaling
More informationA Comparison of Barostats for the Mechanical. Characterization of Metal Organic Frameworks
A Comparison of Barostats for the Mechanical Characterization of Metal Organic Frameworks S.M.J. Rogge, L. Vanduyfhuys, A. Ghysels, M. Waroquier, T. Verstraelen, G. Maurin, and V. Van Speybroeck, Center
More informationUnderstanding Molecular Simulation 2009 Monte Carlo and Molecular Dynamics in different ensembles. Srikanth Sastry
JNCASR August 20, 21 2009 Understanding Molecular Simulation 2009 Monte Carlo and Molecular Dynamics in different ensembles Srikanth Sastry Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore
More informationSupporting Information
Supporting Information Solid-State 17 O NMR Reveals Hydrogen-Bonding Energetics: Not All Low-Barrier Hydrogen Bonds Are Strong Jiasheng Lu, Ivan Hung, Andreas Brinkmann, Zhehong Gan, Xianqi Kong, and Gang
More informationAccelerated Quantum Molecular Dynamics
Accelerated Quantum Molecular Dynamics Enrique Martinez, Christian Negre, Marc J. Cawkwell, Danny Perez, Arthur F. Voter and Anders M. N. Niklasson Outline Quantum MD Current approaches Challenges Extended
More informationNosé-Hoover chain method for nonequilibrium molecular dynamics simulation
PHYSICAL REVIEW E VOLUME 61, NUMBER 5 MAY 000 Nosé-Hoover chain method for nonequilibrium molecular dynamics simulation A. C. Brańka Institute of Molecular Physics, Polish Academy of Sciences, Smoluchowskiego
More informationGear methods I + 1/18
Gear methods I + 1/18 Predictor-corrector type: knowledge of history is used to predict an approximate solution, which is made more accurate in the following step we do not want (otherwise good) methods
More informationFrom Molecular Dynamics to hydrodynamics a novel Galilean invariant thermostat
To appear in: Journal of Chemical Physics, 08 APR 005 From Molecular Dynamics to hydrodynamics a novel Galilean invariant thermostat Simeon D. Stoyanov and Robert D. Groot Unilever Research Vlaardingen,
More informationApproach to Thermal Equilibrium in Biomolecular
Approach to Thermal Equilibrium in Biomolecular Simulation Eric Barth 1, Ben Leimkuhler 2, and Chris Sweet 2 1 Department of Mathematics Kalamazoo College Kalamazoo, Michigan, USA 49006 2 Centre for Mathematical
More informationExploring the anomalous behavior of metal nanocatalysts with finite temperature AIMD and x-ray spectra
Exploring the anomalous behavior of metal nanocatalysts with finite temperature AIMD and x-ray spectra F.D. Vila DOE grant DE-FG02-03ER15476 With computer support from DOE - NERSC. Importance of Theoretical
More informationAb Initio modelling of structural and electronic. Matt Probert University of York
Ab Initio modelling of structural and electronic properties of semiconductors Matt Probert University of York http://www-users.york.ac.uk/~mijp1 Overview of Talk What is Ab Initio? What can we model? How
More informationA path integral approach to the Langevin equation
A path integral approach to the Langevin equation - Ashok Das Reference: A path integral approach to the Langevin equation, A. Das, S. Panda and J. R. L. Santos, arxiv:1411.0256 (to be published in Int.
More informationAb initio phonon calculations in mixed systems
Ab initio phonon calculations in mixed systems Andrei Postnikov apostnik@uos.de Outline: Experiment vs. ab initio theory Ways of theory: linear response and frozen phonon approaches Applications: Be x
More informationComparison of model potentials for molecular dynamics simulation of crystalline silica
Comparison of model potentials for molecular dynamics simulation of crystalline silica Dissertation zur Erlangung des Grades,,Doktor der Naturwissenschaften am Fachbereich Physik der Johannes Gutenberg
More informationA Nobel Prize for Molecular Dynamics and QM/MM What is Classical Molecular Dynamics? Simulation of explicit particles (atoms, ions,... ) Particles interact via relatively simple analytical potential
More informationThe micro-properties of [hmpy+] [Tf 2 N-] Ionic liquid: a simulation. study. 1. Introduction
ISBN 978-1-84626-081-0 Proceedings of the 2010 International Conference on Application of Mathematics and Physics Volume 1: Advances on Space Weather, Meteorology and Applied Physics Nanjing, P. R. China,
More informationPractical Guide to Density Functional Theory (DFT)
Practical Guide to Density Functional Theory (DFT) Brad Malone, Sadas Shankar Quick recap of where we left off last time BD Malone, S Shankar Therefore there is a direct one-to-one correspondence between
More informationand strong interlayer quantum confinement
Supporting Information GeP3: A small indirect band gap 2D crystal with high carrier mobility and strong interlayer quantum confinement Yu Jing 1,3, Yandong Ma 1, Yafei Li 2, *, Thomas Heine 1,3 * 1 Wilhelm-Ostwald-Institute
More information10: Testing Testing. Basic procedure to validate calculations
The Nuts and Bolts of First-Principles Simulation 10: Testing Testing. Basic procedure to validate calculations Durham, 6th-13th December 2001 CASTEP Developers Group with support from the ESF ψ k Network
More informationSupporting Information for. Dynamics Study"
Supporting Information for "CO 2 Adsorption and Reactivity on Rutile TiO 2 (110) in Water: An Ab Initio Molecular Dynamics Study" Konstantin Klyukin and Vitaly Alexandrov,, Department of Chemical and Biomolecular
More informationCHE3935. Lecture 4 Quantum Mechanical Simulation Methods Continued
CHE3935 Lecture 4 Quantum Mechanical Simulation Methods Continued 1 OUTLINE Review Introduction to CPMD MD and ensembles The functionals of density functional theory Return to ab initio methods Binding
More informationLECTURE 6 : BASICS FOR MOLECULAR SIMULATIONS - Historical perspective - Skimming over Statistical Mechanics - General idea of Molecular Dynamics -
LECTURE 6 : BASICS FOR MOLECULAR SIMULATIONS - Historical perspective - Skimming over Statistical Mechanics - General idea of Molecular Dynamics - Force calculations, structure of MD, equations of motion
More informationSupporting Information
Projection of atomistic simulation data for the dynamics of entangled polymers onto the tube theory: Calculation of the segment survival probability function and comparison with modern tube models Pavlos
More informationMolecular Dynamics Simulations. Dr. Noelia Faginas Lago Dipartimento di Chimica,Biologia e Biotecnologie Università di Perugia
Molecular Dynamics Simulations Dr. Noelia Faginas Lago Dipartimento di Chimica,Biologia e Biotecnologie Università di Perugia 1 An Introduction to Molecular Dynamics Simulations Macroscopic properties
More informationTwo recent works on molecular systems out of equilibrium
Two recent works on molecular systems out of equilibrium Frédéric Legoll ENPC and INRIA joint work with M. Dobson, T. Lelièvre, G. Stoltz (ENPC and INRIA), A. Iacobucci and S. Olla (Dauphine). CECAM workshop:
More informationHigh Temperature High Pressure Properties of Silica From Quantum Monte Carlo
High Temperature High Pressure Properties of Silica From Quantum Monte Carlo K.P. Driver, R.E. Cohen, Z. Wu, B. Militzer, P. Lopez Rios, M. Towler, R. Needs, and J.W. Wilkins Funding: NSF, DOE; Computation:
More informationBiomolecular modeling I
2015, December 15 Biomolecular simulation Elementary body atom Each atom x, y, z coordinates A protein is a set of coordinates. (Gromacs, A. P. Heiner) Usually one molecule/complex of interest (e.g. protein,
More information2. TranSIESTA 1. SIESTA. DFT In a Nutshell. Introduction to SIESTA. Boundary Conditions: Open systems. Greens functions and charge density
1. SIESTA DFT In a Nutshell Introduction to SIESTA Atomic Orbitals Capabilities Resources 2. TranSIESTA Transport in the Nanoscale - motivation Boundary Conditions: Open systems Greens functions and charge
More informationChapter 1 Introduction
Chapter 1 Introduction This thesis is concerned with the behaviour of polymers in flow. Both polymers in solutions and polymer melts will be discussed. The field of research that studies the flow behaviour
More informationDynamic force matching: Construction of dynamic coarse-grained models with realistic short time dynamics and accurate long time dynamics
for resubmission Dynamic force matching: Construction of dynamic coarse-grained models with realistic short time dynamics and accurate long time dynamics Aram Davtyan, 1 Gregory A. Voth, 1 2, a) and Hans
More informationAb Initio Molecular Dynamic
Ab Initio Molecular Dynamic Paul Fleurat-Lessard AtoSim Master / RFCT Ab Initio Molecular Dynamic p.1/67 Summary I. Introduction II. Classical Molecular Dynamic III. Ab Initio Molecular Dynamic (AIMD)
More informationAb Initio Molecular Dynamic
Ab Initio Molecular Dynamic Paul Fleurat-Lessard AtoSim Master Ab Initio Molecular Dynamic p.1/67 Summary I. Introduction II. Classical Molecular Dynamic III. Ab Initio Molecular Dynamic (AIMD) 1 - Which
More informationOrganization of NAMD Tutorial Files
Organization of NAMD Tutorial Files .1.1. RMSD for individual residues Objective: Find the average RMSD over time of each residue in the protein using VMD. Display the protein with the residues colored
More informationAn alternative approach to dissipative particle dynamics
EUROPHYSICS LETTERS 15 July 1999 Europhys. Lett., 47 (2), pp. 145-151 (1999) An alternative approach to dissipative particle dynamics C. P. Lowe Computational Physics, Delft University of Technology Lorentzweg
More informationUniversal Repulsive Contribution to the. Solvent-Induced Interaction Between Sizable, Curved Hydrophobes: Supporting Information
Universal Repulsive Contribution to the Solvent-Induced Interaction Between Sizable, Curved Hydrophobes: Supporting Information B. Shadrack Jabes, Dusan Bratko, and Alenka Luzar Department of Chemistry,
More informationRustam Z. Khaliullin University of Zürich
Rustam Z. Khaliullin University of Zürich Molecular dynamics (MD) MD is a computational method for simulating time evolution of a collection of interacting atoms by numerically integrating Newton s equation
More informationCalculating Vibrational Spectra from Molecular Dynamics
Calculating Vibrational Spectra from Molecular Dynamics A Simulating a Trajectory with Wannier Centers To calculate IR spectra from Molecular Dynamics, it is necessary to have dipole information for the
More informationMultiscale Materials Modeling
Multiscale Materials Modeling Lecture 02 Capabilities of Classical Molecular Simulation These notes created by David Keffer, University of Tennessee, Knoxville, 2009. Outline Capabilities of Classical
More informationFor info and ordering all the 4 versions / languages of this book please visit: http://trl.lab.uic.edu/pon Contents Preface vii Chapter 1 Advances in Atomic and Molecular Nanotechnology Introduction 1
More informationMesoscale Simulation Methods. Ronojoy Adhikari The Institute of Mathematical Sciences Chennai
Mesoscale Simulation Methods Ronojoy Adhikari The Institute of Mathematical Sciences Chennai Outline What is mesoscale? Mesoscale statics and dynamics through coarse-graining. Coarse-grained equations
More informationIntroduction to model potential Molecular Dynamics A3hourcourseatICTP
Introduction to model potential Molecular Dynamics A3hourcourseatICTP Alessandro Mattoni 1 1 Istituto Officina dei Materiali CNR-IOM Unità di Cagliari SLACS ICTP School on numerical methods for energy,
More informationComputer simulations of soft repulsive spherocylinders
MOLECULAR PHYSICS, 2001, VOL. 99, NO. 20, 1719± 1726 Computer simulations of soft repulsive spherocylinders DAVID J. EARL, JAROSLAV ILNYTSKYI and MARK R. WILSON* Department of Chemistry, University of
More informationElectronic structure and transport in silicon nanostructures with non-ideal bonding environments
Purdue University Purdue e-pubs Other Nanotechnology Publications Birck Nanotechnology Center 9-15-2008 Electronic structure and transport in silicon nanostructures with non-ideal bonding environments
More informationChaotic Modeling and Simulation (CMSIM) 2: , 2017
Chaotic Modeling and Simulation (CMSIM) 2: 205-212, 2017 Bifurcation based parameter selection of PBD model in DNA Sohrab Behnia 1, Robabeh Panahinia 1 1 Faculty of physics, Urmia University of Technology,
More informationSilica glass structure generation for ab initio calculations using small samples of amorphous silica
Silica glass structure generation for ab initio calculations using small samples of amorphous silica Renée M. Van Ginhoven* University of Washington, Seattle, Washington 98512, USA Hannes Jónsson University
More informationCrossing the barriers - simulations of activated processes
Crossing the barriers - simulations of activated processes Mgr. Ján Hreha for 6 th Student Colloquium and School on Mathematical Physics Faculty of Mathematics, Physics and Informatics Comenius University
More informationHands-on : Model Potential Molecular Dynamics
Hands-on : Model Potential Molecular Dynamics OUTLINE 0. DL_POLY code introduction 0.a Input files 1. THF solvent molecule 1.a Geometry optimization 1.b NVE/NVT dynamics 2. Liquid THF 2.a Equilibration
More informationMechanical Properties of Tetra-Polyethylene and Tetra-Polyethylene Oxide Diamond Networks via Molecular Dynamics Simulations
Supplemental Information Mechanical Properties of Tetra-Polyethylene and Tetra-Polyethylene Oxide Diamond Networks via Molecular Dynamics Simulations Endian Wang and Fernando A. Escobedo Table S1 Lennard-Jones
More informationEquilibrium molecular dynamics studies on nanoscale-confined fluids
DOI 10.1007/s10404-011-0794-5 RESEARCH PAPER Equilibrium molecular dynamics studies on nanoscale-confined fluids Murat Barisik Ali Beskok Received: 26 January 2011 / Accepted: 18 March 2011 Ó Springer-Verlag
More information