Difference between revisions of "Simulationsmethoden II SS2010"
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:Prof. Dr. [[Christian Holm]] (Lecture) and [[Joan Josep Cerdà]], [[Nadezhda Gribova]] (Tutorials)  :Prof. Dr. [[Christian Holm]] (Lecture) and [[Joan Josep Cerdà]], [[Nadezhda Gribova]] (Tutorials)  
;Course language  ;Course language  
−  :English  +  :English or German, depending on audience 
;Time and Room  ;Time and Room  
−  :Lecture times:  +  :Lecture times: Wednesday, 9:45 a.m.11:15 pa.m., V27.03, Pfaffenwaldring 27 
:Tutorial times: Wednesday, 3:30 p.m.5:30 p.m., Room U 108 (Pfaffenwaldring 27)  :Tutorial times: Wednesday, 3:30 p.m.5:30 p.m., Room U 108 (Pfaffenwaldring 27)  
The lecture is accompanied by handsontutorials which will take place in the CIPPool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.  The lecture is accompanied by handsontutorials which will take place in the CIPPool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis.  
−  The tutorials build on each other, therefore continuous attendance is expected.  +  The tutorials build on each other, therefore continuous attendance is expected. The solutions to the worksheet will be handed in and graded, 
==Scope==  ==Scope==  
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lecture will consist of:  lecture will consist of:  
−  '''1. '''  +  '''1. ''' Biomolecular Simulation Approaches 
−  '''2. '''  +  '''2. ''' Coarse Graining Strategies for Soft Matter 
−  '''3. '''  +  '''3. ''' Efficient Methods for Treating Long Range Interactions 
−  '''4. '''  +  '''4. ''' Free Energy Calculations 
+  
+  '''5. ''' Advanced Monte Carlo Methods  
== Prerequisites ==  == Prerequisites ==  
We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language (preferably C or C++).  We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language (preferably C or C++).  
+  The successful attendence of the previous course Simulation methods I is required, since we will build up the lecture on previously gained knowledge.  
== Certificate Requirements:==  == Certificate Requirements:==  
+  There will be a final grade for the Modul "Simulation Methods" determined at the end of this course.  
+  
+  The final grade will be determined in the following way :  
−  +  :1. 50% comes from the marks for the handin exercises for ''' both''' parts of the course (Simulation Methods in Physics I and II)  
+  These are determined by the best marks obtained in 6 out of 7 tutorials in Sim I plus all accumulated marks of all 6 tutorials in Sim II.  
−  :  +  :2. 50% will be determined in an oral examination performed at (or after) the end of the course. 
−  
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!Date !! Subject  !Date !! Subject  
    
−    +  21.04.10  Intro to ''in silicio'' Biology 
    
−    +   28.04.10  Abinitio QM Methods 
    
−    +   05.05.10  DFT Methods, Water models 
    
−    +   12.05.10  Born Model, Simulating Macromolecules 
    
−    +   19.05.10  Implicit Solvent Model, BeadSpring Model 
    
−    +   02.06.10  Coarsegrained models for macromolecules 
    
−    +   09.06.10  Treating longrange interaction in periodic geometries, <br>Introduction to PoissonBoltzmann theory 
    
−    +   16.06.10  PoissonBoltzmann theory, polyelectrolytes and charged colloids {{DownloadLecture7.pdfPDF}} <br> also look at ''M. Deserno and C. Holm: [http://www.ica1.unistuttgart.de/~icp/bib/pdf/icp/deserno01c.pdf Cellmodel and PoissonBoltzmanntheory: <br>A brief introduction]'' 
    
−    +   23.06.10  Hydrodynamic Interactions: Brownian Dynamics, LatticeBoltzmann Methods 
    
−    +   30.06.10  Dissipative Particle Dynamics 
    
−    +   07.07.10  Free Energy Calculations 
    
−    +   14.07.10  Advanced Monte Carlo Simulations: Parallel Tempering 
    
−    +   21.07.10  Advanced Monte Carlo Simulations: Reweighting 
    
}  }  
Line 79:  Line 85:  
!Date !! Subject  !Date !! Subject  
    
−  21.04/28.04  Error Analysis.  +  21.04/28.04  [[Error Analysis.]] 
    
05.05/12.05  Atomistic simulations using GROMACS package. Water models.  05.05/12.05  Atomistic simulations using GROMACS package. Water models. 
Latest revision as of 13:23, 28 July 2010
Overview
Simulationsmethoden in der Physik II: Simulation Methods in Physics II
 Type
 Lecture (2 SWS) and Tutorials (1 SWS)
 Lecturer
 Prof. Dr. Christian Holm (Lecture) and Joan Josep Cerdà, Nadezhda Gribova (Tutorials)
 Course language
 English or German, depending on audience
 Time and Room
 Lecture times: Wednesday, 9:45 a.m.11:15 pa.m., V27.03, Pfaffenwaldring 27
 Tutorial times: Wednesday, 3:30 p.m.5:30 p.m., Room U 108 (Pfaffenwaldring 27)
The lecture is accompanied by handsontutorials which will take place in the CIPPool of the ICP, Pfaffenwaldring 27, U 108. They consist of practical exercises at the computer, like small programming tasks, simulations, visualization and data analysis. The tutorials build on each other, therefore continuous attendance is expected. The solutions to the worksheet will be handed in and graded,
Scope
The course intends to give an overview about modern simulation methods used in physics today. The stress of the lecture will be to introduce different approaches to simulate a problem, hence we will not go too to deep into specific details but rather try to cover a broad range of methods. In more detail, the lecture will consist of:
1. Biomolecular Simulation Approaches
2. Coarse Graining Strategies for Soft Matter
3. Efficient Methods for Treating Long Range Interactions
4. Free Energy Calculations
5. Advanced Monte Carlo Methods
Prerequisites
We expect the participants to have basic knowledge in classical and statistical mechanics, thermodynamics, electrodynamics, and partial differential equations, as well as knowledge of a programming language (preferably C or C++). The successful attendence of the previous course Simulation methods I is required, since we will build up the lecture on previously gained knowledge.
Certificate Requirements:
There will be a final grade for the Modul "Simulation Methods" determined at the end of this course.
The final grade will be determined in the following way :
 1. 50% comes from the marks for the handin exercises for both parts of the course (Simulation Methods in Physics I and II)
These are determined by the best marks obtained in 6 out of 7 tutorials in Sim I plus all accumulated marks of all 6 tutorials in Sim II.
 2. 50% will be determined in an oral examination performed at (or after) the end of the course.
Lecture
Date  Subject 

28.04.10  Abinitio QM Methods 
05.05.10  DFT Methods, Water models 
12.05.10  Born Model, Simulating Macromolecules 
19.05.10  Implicit Solvent Model, BeadSpring Model 
02.06.10  Coarsegrained models for macromolecules 
09.06.10  Treating longrange interaction in periodic geometries, Introduction to PoissonBoltzmann theory 
16.06.10  PoissonBoltzmann theory, polyelectrolytes and charged colloids PDF (6.08 MB) also look at M. Deserno and C. Holm: Cellmodel and PoissonBoltzmanntheory: A brief introduction 
23.06.10  Hydrodynamic Interactions: Brownian Dynamics, LatticeBoltzmann Methods 
30.06.10  Dissipative Particle Dynamics 
07.07.10  Free Energy Calculations 
14.07.10  Advanced Monte Carlo Simulations: Parallel Tempering 
21.07.10  Advanced Monte Carlo Simulations: Reweighting 
Tutorials (U 108)
Date  Subject 

21.04/28.04  Error Analysis. 
05.05/12.05  Atomistic simulations using GROMACS package. Water models. 
19.05/02.06  Introduction to ESPResSo package. Simulation of a polymer. 
16.06/23.06  Simulation of a charged rod. 
30.06/07.07  Lattice Bolzmann. 
14.07/21.07  Advanced MD. 
Recommended literature

Daan Frenkel and Berend Smit.
"Understanding Molecular Simulation".
Academic Press, San Diego, 2002.
[DOI] 
Mike P. Allen and Dominik J. Tildesley.
"Computer Simulation of Liquids".
Oxford Science Publications, Clarendon Press, Oxford, 1987.

Rapaport, D. C..
"The Art of Molecular Dynamics Simulation".
Cambridge University Press, 2004.
[DOI] 
D. P. Landau and K. Binder.
"A guide to Monte Carlo Simulations in Statistical Physics".
Cambridge, 2005.

M. E. J. Newman and G. T. Barkema.
"Monte Carlo Methods in Statistical Physics".
Oxford University Press, 1999.

Hans Jörg Limbach and Axel Arnold and B. A. Mann and Christian Holm.
"ESPResSo – An Extensible Simulation Package for Research on Soft Matter Systems".
Computer Physics Communications 174(9)(704–727), 2006.
[PDF] (318 KB) [DOI]
Available EBooks
D.P. Landau and K. Binder.